Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007963.1 Hibiscus syriacus cultivar Beakdansim tig00110392_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1627826
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 7
Found at i:241717 original size:19 final size:18
Alignment explanation
Indices: 241655--241717 Score: 65
Period size: 20 Copynumber: 3.3 Consensus size: 18
241645 TTGACCCCCC
241655 TTTTTCT-TTTTCTTTTTT
1 TTTTTCTCTTTT-TTTTTT
*
241673 CTTTTCTCTTTTTTTCTTTCT
1 TTTTTCTC-TTTTTT-TTT-T
241694 TTTTTCTCTTTTTTTTCTT
1 TTTTTCTCTTTTTTTT-TT
241713 TTTTT
1 TTTTT
241718 TCAAGCATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
18 6 0.16
19 10 0.26
20 14 0.37
21 8 0.21
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (18 bp):
TTTTTCTCTTTTTTTTTT
Found at i:248934 original size:15 final size:15
Alignment explanation
Indices: 248911--248942 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
248901 TGAAATGAAT
248911 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
248926 AATGCATGTATGCAA
1 AATGAATGTATGCAA
248941 AA
1 AA
248943 AGGTATTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:252953 original size:12 final size:12
Alignment explanation
Indices: 252930--252972 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
252920 CTTTTCTTCG
252930 ATATTGAAAATAA
1 ATATT-AAAATAA
*
252943 ATGTTAAAATAA
1 ATATTAAAATAA
*
252955 TTTATTAAAATAA
1 -ATATTAAAATAA
252968 ATATT
1 ATATT
252973 TATTTATTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
12 11 0.44
13 14 0.56
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.40
Consensus pattern (12 bp):
ATATTAAAATAA
Found at i:254390 original size:3 final size:3
Alignment explanation
Indices: 254382--254431 Score: 57
Period size: 3 Copynumber: 16.3 Consensus size: 3
254372 GGCCTGGTTG
* *
254382 TAA TAA TAA TAT TAA TAA TAA AAA TATA TAA TAAA TAA T-A TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA T-AA TAA TAA TAA TAA
254428 TAA T
1 TAA T
254432 TATTATAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
2 2 0.05
3 32 0.80
4 6 0.15
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:254438 original size:15 final size:14
Alignment explanation
Indices: 254382--254439 Score: 59
Period size: 15 Copynumber: 4.2 Consensus size: 14
254372 GGCCTGGTTG
254382 TAATAATAATATTAA
1 TAATAATAATATT-A
*
254397 TAATAAAAATA-TA
1 TAATAATAATATTA
*
254410 TAAT-A-AATAATA
1 TAATAATAATATTA
254422 TAATAATAATTATTA
1 TAATAATAA-TATTA
254437 TAA
1 TAA
254440 AACCGGGACA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
11 4 0.11
12 7 0.19
13 6 0.16
14 3 0.08
15 17 0.46
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
TAATAATAATATTA
Found at i:254926 original size:72 final size:73
Alignment explanation
Indices: 254869--255042 Score: 214
Period size: 74 Copynumber: 2.4 Consensus size: 73
254859 GAAACTTTAA
*
254869 TATATTTTCAAAAATATAT-A-ACATATTATTTTTGAAATTATATA-ATAT-TTTTAAATATATA
1 TATATTTTCAAAAATATATAATACATATTATTTTTAAAATTATATAGATATATTTTAAATATATA
254930 TAAATAATG
66 TAAATAA-G
*
254939 TATATTTTCAAAAATATATAATATATATTATTTTTAAAATTATATAGTATATATTTT-AATATAT
1 TATATTTTCAAAAATATATAATACATATTATTTTTAAAATTATATAG-ATATATTTTAAATATAT
*
255003 ATATATATAG
65 ATAAATA-AG
* * *
255013 TATATACTTTTAAAACTATATAATATATAT
1 TATAT--TTTCAAAAATATATAATACATAT
255043 ATATATATAT
Statistics
Matches: 91, Mismatches: 5, Indels: 10
0.86 0.05 0.09
Matches are distributed among these distances:
70 19 0.21
71 1 0.01
72 22 0.24
74 23 0.25
75 5 0.05
76 21 0.23
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (73 bp):
TATATTTTCAAAAATATATAATACATATTATTTTTAAAATTATATAGATATATTTTAAATATATA
TAAATAAG
Found at i:254927 original size:17 final size:19
Alignment explanation
Indices: 254895--254932 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
254885 TATAACATAT
254895 TATTTTTGAAATTATATAA
1 TATTTTTGAAATTATATAA
254914 TATTTTT-AAATATATATAA
1 TATTTTTGAAAT-TATATAA
254933 ATAATGTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (19 bp):
TATTTTTGAAATTATATAA
Found at i:254961 original size:26 final size:25
Alignment explanation
Indices: 254868--255171 Score: 150
Period size: 25 Copynumber: 12.0 Consensus size: 25
254858 CGAAACTTTA
* *
254868 ATATATTTTCAAAAATATATAACAT
1 ATATATTTTTAAAAATATATAATAT
*
254893 AT-TATTTTT--GAA-AT-T-ATAT
1 ATATATTTTTAAAAATATATAATAT
*
254912 A-ATATTTTTAAATATATATAAATAAT
1 ATATATTTTTAAAAATATAT-AAT-AT
* *
254938 GTATATTTTCAAAAATATATAATAT
1 ATATATTTTTAAAAATATATAATAT
254963 ATATTATTTTT-AAAAT-TAT-ATAGT
1 ATA-TATTTTTAAAAATATATAATA-T
*
254987 ATATA-TTTTAATATATATATATATAGT
1 ATATATTTTTAA-AAATATATA-ATA-T
* *
255014 ATATACTTTTAAAACTATATAATAT
1 ATATATTTTTAAAAATATATAATAT
* ** * *
255039 ATATATATATATATTATTTTCATAATAAT
1 ATATAT-T-TTTAAAAATAT-ATAAT-AT
* *
255068 ATAATATGTACTTTCAAAACTCTATAATAT
1 AT-ATAT-T--TTT-AAAAATATATAATAT
*
255098 ATATTATTTTTAAAATTATAT-A-AT
1 ATA-TATTTTTAAAAATATATAATAT
*
255122 ATATATTTTAAAAATATATATAATA-
1 ATATATTTTTAAAA-ATATATAATAT
* * *
255147 ATATAATTTCAAACTATATATAATA
1 ATATATTTTTAAA-AATATATAATA
255172 GATCATTATA
Statistics
Matches: 217, Mismatches: 33, Indels: 58
0.70 0.11 0.19
Matches are distributed among these distances:
19 11 0.05
20 1 0.00
21 3 0.01
22 8 0.04
23 17 0.08
24 26 0.12
25 45 0.21
26 24 0.11
27 42 0.19
28 11 0.05
29 6 0.03
30 12 0.06
31 7 0.03
32 4 0.02
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (25 bp):
ATATATTTTTAAAAATATATAATAT
Found at i:254984 original size:2 final size:2
Alignment explanation
Indices: 254979--255052 Score: 50
Period size: 2 Copynumber: 37.5 Consensus size: 2
254969 TTTTTAAAAT
*
254979 TA TA TA GTA TA TA T- TT TA -A TA TA TA TA TA TA TA GTA TA TA CT-
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA
* *
255021 TT TA -A AA CTA TA TA -A TA TA TA TA TA TA TA TA T
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA T
255053 TATTTTCATA
Statistics
Matches: 60, Mismatches: 3, Indels: 18
0.74 0.04 0.22
Matches are distributed among these distances:
1 5 0.08
2 49 0.82
3 6 0.10
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:255039 original size:76 final size:72
Alignment explanation
Indices: 254868--255042 Score: 230
Period size: 76 Copynumber: 2.4 Consensus size: 72
254858 CGAAACTTTA
* *
254868 ATATATTTTCAAAAATATAT-A-ACATATTATTTTTGAAATTATATAATATTTTTAAATATATAT
1 ATATATTTTCAAAAATATATAATATATATTATTTTTAAAATTATATAATATTTTTAAATATATAT
254931 AAATAAT
66 AAATAAT
*
254938 GTATATTTTCAAAAATATATAATATATATTATTTTTAAAATTATATAGTATATATTTTAATATAT
1 ATATATTTTCAAAAATATATAATATATATTATTTTTAAAATTATATA--ATAT-TTTTAA-ATAT
* *
255003 ATATATATAGT
62 ATATAAATAAT
*
255014 ATATACTTTT-AAAACTATATAATATATAT
1 ATATA-TTTTCAAAAATATATAATATATAT
255043 ATATATATAT
Statistics
Matches: 91, Mismatches: 7, Indels: 8
0.86 0.07 0.08
Matches are distributed among these distances:
70 19 0.21
71 1 0.01
72 22 0.24
74 4 0.04
75 6 0.07
76 35 0.38
77 4 0.04
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (72 bp):
ATATATTTTCAAAAATATATAATATATATTATTTTTAAAATTATATAATATTTTTAAATATATAT
AAATAAT
Found at i:255081 original size:59 final size:63
Alignment explanation
Indices: 254979--255101 Score: 166
Period size: 59 Copynumber: 2.0 Consensus size: 63
254969 TTTTTAAAAT
*
254979 TATATAGTATATATTTTAATATATATATATATAGTATATACTTTTAAAACTATATAATATATA
1 TATATAGTATATATTTTAATATATATATATATAGTATATACTTTCAAAACTATATAATATATA
* * *
255042 TATATA-TATATTATTTTCATA-ATA-ATATA-A-TATGTACTTTCAAAACTCTATAATATATA
1 TATATAGTATA-TATTTTAATATATATATATATAGTATATACTTTCAAAACTATATAATATATA
255101 T
1 T
255102 TATTTTTAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
59 27 0.49
60 1 0.02
61 5 0.09
62 7 0.13
63 15 0.27
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.47
Consensus pattern (63 bp):
TATATAGTATATATTTTAATATATATATATATAGTATATACTTTCAAAACTATATAATATATA
Found at i:255136 original size:23 final size:23
Alignment explanation
Indices: 254868--255042 Score: 101
Period size: 23 Copynumber: 7.3 Consensus size: 23
254858 CGAAACTTTA
*
254868 ATATATTTTCAAAAA-TATATAAC
1 ATATATTTT-AAAAATTATATAAT
**
254891 ATATTATTTTTGAAATTATAT-A-
1 ATA-TATTTTAAAAATTATATAAT
*
254913 ATAT-TTTTAAATATATATAAATAAT
1 ATATATTTTAAA-A-AT-TATATAAT
*
254938 GTATATTTTCAAAAA-TATATAATAT
1 ATATATTTT-AAAAATTATAT-A-AT
* *
254963 ATATTATTTTTAAAATTATATAGT
1 ATA-TATTTTAAAAATTATATAAT
*
254987 ATATATTTTAATATATATATATATAGT
1 ATATATTTTAA-A-A-AT-TATATAAT
*
255014 ATATACTTTT-AAAACTATATAAT
1 ATATA-TTTTAAAAATTATATAAT
255037 ATATAT
1 ATATAT
255043 ATATATATAT
Statistics
Matches: 121, Mismatches: 13, Indels: 37
0.71 0.08 0.22
Matches are distributed among these distances:
20 5 0.04
21 2 0.02
22 6 0.05
23 34 0.28
24 19 0.16
25 15 0.12
26 19 0.16
27 17 0.14
28 4 0.03
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (23 bp):
ATATATTTTAAAAATTATATAAT
Found at i:255186 original size:135 final size:134
Alignment explanation
Indices: 254944--255189 Score: 345
Period size: 135 Copynumber: 1.8 Consensus size: 134
254934 TAATGTATAT
* *
254944 TTTCAAAAATATATAATATATATTATTTTTAAAATTATATAGTATATATTTTAATATATATATAT
1 TTTCAAAAATATATAATATATATTATTTTTAAAATTATATAATATATATTTTAAAATATATATAT
* * *
255009 ATAGTATATACTTTTAAAACTATATAATATATATATATATATATTATTTTCATAATAATATAATA
66 ATAG-ATATAATTTCAAAACTATATAATAGATATATATATATATTATTTTCATAATAATATAATA
255074 TGTAC
130 TGTAC
* *
255079 TTTCAAAACTCTATAATATATATTATTTTTAAAATTATATAATATATATTTTAAAA-ATATATAT
1 TTTCAAAAATATATAATATATATTATTTTTAAAATTATATAATATATATTTTAAAATATATATAT
255143 AATA-ATATAATTTC-AAACTATATATAATAGATCATTATAATATATAT
66 -ATAGATATAATTTCAAAAC--TATATAATAGAT-A-TAT-ATATATAT
255190 AGTAGTACGT
Statistics
Matches: 98, Mismatches: 7, Indels: 10
0.85 0.06 0.09
Matches are distributed among these distances:
132 4 0.04
133 8 0.08
134 19 0.19
135 56 0.57
136 3 0.03
137 8 0.08
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (134 bp):
TTTCAAAAATATATAATATATATTATTTTTAAAATTATATAATATATATTTTAAAATATATATAT
ATAGATATAATTTCAAAACTATATAATAGATATATATATATATTATTTTCATAATAATATAATAT
GTAC
Found at i:256039 original size:16 final size:16
Alignment explanation
Indices: 255998--256043 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
255988 TTAAAATTAG
255998 ATATTATTTTA-AATA
1 ATATTATTTTACAATA
*
256013 ATTTTATTTTTACAATA
1 ATATTA-TTTTACAATA
256030 ATATTATTTTACAA
1 ATATTATTTTACAA
256044 CTCATAAAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
15 5 0.19
16 13 0.48
17 9 0.33
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.54
Consensus pattern (16 bp):
ATATTATTTTACAATA
Found at i:256217 original size:23 final size:23
Alignment explanation
Indices: 256174--256223 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
256164 ATCACTTTAT
* *
256174 TTAA-AAACTTTTCGGTTGCCAA
1 TTAATAAACTTTTCAGTGGCCAA
*
256196 TTAATAAATTTTTCAGTGGCCAA
1 TTAATAAACTTTTCAGTGGCCAA
256219 TTAAT
1 TTAAT
256224 TCACTTCAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 4 0.17
23 20 0.83
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.40
Consensus pattern (23 bp):
TTAATAAACTTTTCAGTGGCCAA
Found at i:256396 original size:104 final size:104
Alignment explanation
Indices: 256216--256431 Score: 303
Period size: 104 Copynumber: 2.1 Consensus size: 104
256206 TTTCAGTGGC
* * * * *
256216 CAATTAATTCACTTCAGACACTTTTTATGGATATATCACTTCATTTCATAAACGTTTTAGTGATA
1 CAATTAATTCAATTCAGACACTTTTCATGCATATATCACTTCATTTCAAAAACGTTTTAATGATA
* * *
256281 TATAAATTCATTTCAGAAAAACG-TCGTTTTCTCTTACAA
66 AATAAATTCATTTCAGAAAAACGTTC-TTCTCTCATACAA
*
256320 CAATTAATT-AATGTCAGACACTTTTCATTCATATATCACTTCATTTCAAAAAC-TTTTCAATGA
1 CAATTAATTCAAT-TCAGACACTTTTCATGCATATATCACTTCATTTCAAAAACGTTTT-AATGA
256383 TAAATAAATTCATTTCAGAAAAACGTTCTTCTCTCATACAA
64 TAAATAAATTCATTTCAGAAAAACGTTCTTCTCTCATACAA
256424 CAATTAAT
1 CAATTAAT
256432 ACACAACGAC
Statistics
Matches: 100, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
103 6 0.06
104 92 0.92
105 2 0.02
ACGTcount: A:0.37, C:0.18, G:0.06, T:0.39
Consensus pattern (104 bp):
CAATTAATTCAATTCAGACACTTTTCATGCATATATCACTTCATTTCAAAAACGTTTTAATGATA
AATAAATTCATTTCAGAAAAACGTTCTTCTCTCATACAA
Found at i:260157 original size:16 final size:16
Alignment explanation
Indices: 260138--260187 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 16
260128 ATTTAATAAT
260138 ATAATATATATATATA
1 ATAATATATATATATA
260154 ATAATAT-T-TA-ATA
1 ATAATATATATATATA
* *
260167 ATAATA-ATAAATTTA
1 ATAATATATATATATA
260182 ATAATA
1 ATAATA
260188 ATTTAAGTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
13 10 0.34
14 3 0.10
15 9 0.31
16 7 0.24
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATAATATATATATATA
Found at i:260157 original size:21 final size:19
Alignment explanation
Indices: 260119--260186 Score: 59
Period size: 19 Copynumber: 3.4 Consensus size: 19
260109 TTATTTGTAA
*
260119 ATAATAATTATTTAATAAT
1 ATAATAATTATATAATAAT
260138 ATAATATATATATATAATAAT
1 ATAATA-AT-TATATAATAAT
260159 ATTTAATAA-TA-ATAATAAAT
1 A--TAATAATTATATAAT-AAT
*
260179 TTAATAAT
1 ATAATAAT
260187 AATTTAAGTA
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
18 6 0.15
19 11 0.27
20 7 0.17
21 11 0.27
22 1 0.02
23 5 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
ATAATAATTATATAATAAT
Found at i:260182 original size:18 final size:17
Alignment explanation
Indices: 260118--260189 Score: 80
Period size: 16 Copynumber: 4.4 Consensus size: 17
260108 CTTATTTGTA
260118 AATAATAATTATTTAAT
1 AATAATAATTATTTAAT
*
260135 AAT-ATAA-TATAT-AT
1 AATAATAATTATTTAAT
260149 ATATAATAA-TATTTAAT
1 A-ATAATAATTATTTAAT
*
260166 AATAATAATAAATTTAAT
1 AATAATAAT-TATTTAAT
260184 AATAAT
1 AATAAT
260190 TTAAGTAAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
14 3 0.06
15 6 0.13
16 19 0.40
17 6 0.13
18 13 0.28
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AATAATAATTATTTAAT
Found at i:260185 original size:12 final size:11
Alignment explanation
Indices: 260118--260193 Score: 56
Period size: 11 Copynumber: 7.2 Consensus size: 11
260108 CTTATTTGTA
260118 AATAATAA-TT
1 AATAATAATTT
* *
260128 ATTTAATAATAT
1 A-ATAATAATTT
*
260140 AATATATATATAT
1 AATA-ATA-ATTT
260153 AATAAT-ATTT
1 AATAATAATTT
260163 AATAATAA--T
1 AATAATAATTT
260172 AAT-A-AATTT
1 AATAATAATTT
260181 AATAATAATTT
1 AATAATAATTT
260192 AA
1 AA
260194 GTAAAATGAA
Statistics
Matches: 53, Mismatches: 4, Indels: 17
0.72 0.05 0.23
Matches are distributed among these distances:
7 2 0.04
8 1 0.02
9 8 0.15
10 11 0.21
11 16 0.30
12 7 0.13
13 8 0.15
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (11 bp):
AATAATAATTT
Found at i:260198 original size:21 final size:20
Alignment explanation
Indices: 260120--260198 Score: 74
Period size: 18 Copynumber: 3.9 Consensus size: 20
260110 TATTTGTAAA
* *
260120 TAATAATTATTTAAT-AATA
1 TAATAATAATTTAATAAATT
*
260139 TAATATATATATATAATAATATT
1 TAATA-ATA-ATTTAATAA-ATT
260162 TAATAATAA--TAATAAATT
1 TAATAATAATTTAATAAATT
260180 TAATAATAATTTAAGTAAA
1 TAATAATAATTTAA-TAAA
260199 ATGAAAAATT
Statistics
Matches: 50, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
18 12 0.24
19 11 0.22
20 5 0.10
21 11 0.22
22 4 0.08
23 7 0.14
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (20 bp):
TAATAATAATTTAATAAATT
Found at i:260441 original size:76 final size:76
Alignment explanation
Indices: 260343--261891 Score: 2803
Period size: 76 Copynumber: 20.4 Consensus size: 76
260333 GAGGTCGTAA
*
260343 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
260408 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
260419 AAACATCATGCACTACAGGACTTATAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
260484 AGGCTTTTTGG
66 AGGCTTTTTGG
*
260495 AAACATCATGCACTGCAGGACTTATAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
260560 AGGCGTTTTGG
66 AGGCTTTTTGG
*
260571 AAACATCATGCACTGCAGGACTTACAGATGACCCTATGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
260636 AGGCTTTTTGG
66 AGGCTTTTTGG
260647 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
* *
260712 ATGATTTTTGG
66 AGGCTTTTTGG
*
260723 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
260788 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
260799 AAACATCATGCACTACAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
260864 AGGCTTTTTGG
66 AGGCTTTTTGG
260875 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
260940 AGGCTTTTTGG
66 AGGCTTTTTGG
*
260951 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCTA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
261016 AGGCATTTTGG
66 AGGCTTTTTGG
* *
261027 AAACATCATGCACTACAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCTA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
261092 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
261103 AAACATCATGCACTGCAAGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
261168 AGGCTTTTTGG
66 AGGCTTTTTGG
*
261179 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
* *
261244 ATGCGTTTTGG
66 AGGCTTTTTGG
* *
261255 AAACATCATGCACTGCAGAACTTAAAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
261320 AGGCTTTTTGG
66 AGGCTTTTTGG
*
261331 AAACATCATGCACTGCAGGACTTACAGATGAACCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
261396 AGGCTTTTTGG
66 AGGCTTTTTGG
*
261407 AAACATCATGCACTGCAGGACTTACAAATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
261472 AGGCTTTTTGG
66 AGGCTTTTTGG
261483 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGG-TTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
261547 AGGCTTTTTGG
66 AGGCTTTTTGG
261558 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
261623 AGGCTTTTTGG
66 AGGCTTTTTGG
* * *
261634 AAACATCATGCACTGCAAGACTTACAGATGACCCTAAGGTTTTAAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
261699 AGGCTTTTTGG
66 AGGCTTTTTGG
*
261710 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAGAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
261775 AGGCTTATTGG
66 AGGCTTTTTGG
*
261786 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
261851 ATGCTTTTTGG
66 AGGCTTTTTGG
*
261862 AAACATTATGCACTGCAGGACTTACAGATG
1 AAACATCATGCACTGCAGGACTTACAGATG
261892 TGGGAAATAG
Statistics
Matches: 1416, Mismatches: 56, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
75 75 0.05
76 1341 0.95
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (76 bp):
AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:262763 original size:22 final size:22
Alignment explanation
Indices: 262738--262790 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
262728 TAAAGCTTTT
262738 ATCTTTGAAAAGAGAATCTATC
1 ATCTTTGAAAAGAGAATCTATC
*
262760 ATCTTTAAAAAGAGAATCTATC
1 ATCTTTGAAAAGAGAATCTATC
262782 ATCTTTGAA
1 ATCTTTGAA
262791 GAGTGTATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.42, C:0.13, G:0.11, T:0.34
Consensus pattern (22 bp):
ATCTTTGAAAAGAGAATCTATC
Found at i:265430 original size:114 final size:114
Alignment explanation
Indices: 265230--265448 Score: 352
Period size: 114 Copynumber: 1.9 Consensus size: 114
265220 CATGCAGTTT
* * * *
265230 ATCTTTCAATTTCAATGATTGGTTCTGGGGTTCCTACCGAACCAGATCAGATAACTCAAAGAACA
1 ATCTTTCAATCTCAATGATTGGTTCTGAGGTTCATACCAAACCAGATCAGATAACTCAAAGAACA
*
265295 TTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGGGCAAATTC
66 CTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGGGCAAATTC
265344 ATCTTTCAAATCT-AATGATTGGTT-TAGAGGTTCATACCAAACCAGATCAGATAACTCAAAGAA
1 ATCTTTC-AATCTCAATGATTGGTTCT-GAGGTTCATACCAAACCAGATCAGATAACTCAAAGAA
*
265407 CACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATG
64 CACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATG
265449 AGAACGTGGC
Statistics
Matches: 97, Mismatches: 6, Indels: 4
0.91 0.06 0.04
Matches are distributed among these distances:
113 1 0.01
114 92 0.95
115 4 0.04
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.33
Consensus pattern (114 bp):
ATCTTTCAATCTCAATGATTGGTTCTGAGGTTCATACCAAACCAGATCAGATAACTCAAAGAACA
CTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGGGCAAATTC
Found at i:273605 original size:22 final size:25
Alignment explanation
Indices: 273565--273617 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 25
273555 AAATTAATCA
273565 AATAATATATTAATATAATTAAAAT
1 AATAATATATTAATATAATTAAAAT
*
273590 AATAATA-ATT-AT-TAATTTAAAT
1 AATAATATATTAATATAATTAAAAT
273612 ATATAA
1 A-ATAA
273618 CAATAAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
22 10 0.38
23 6 0.23
24 3 0.12
25 7 0.27
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (25 bp):
AATAATATATTAATATAATTAAAAT
Found at i:273662 original size:26 final size:28
Alignment explanation
Indices: 273613--273665 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
273603 AATTTAAATA
273613 TATAACAATAAAATAAAATTGATCAAAAG
1 TATAACAATAAAATAAAA-TGATCAAAAG
*
273642 TATAATAA-AAAATAAAA-GATCAAA
1 TATAACAATAAAATAAAATGATCAAA
273666 TTCGAAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 7 0.30
28 9 0.39
29 7 0.30
ACGTcount: A:0.66, C:0.06, G:0.06, T:0.23
Consensus pattern (28 bp):
TATAACAATAAAATAAAATGATCAAAAG
Found at i:274891 original size:3 final size:3
Alignment explanation
Indices: 274883--274964 Score: 73
Period size: 3 Copynumber: 28.0 Consensus size: 3
274873 CCTGTTTGTA
* *
274883 AAT AAT AAT TAT -TT AAT AAT AAT -AT AAT -AT ATAT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT
* **
274925 AAT AAT ATTT AAT AAT AAT AAT AAT AAT TTT AAT AAT AAT
1 AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
274965 TTAAGTAAAA
Statistics
Matches: 64, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
2 7 0.11
3 52 0.81
4 5 0.08
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (3 bp):
AAT
Found at i:274924 original size:25 final size:22
Alignment explanation
Indices: 274883--274964 Score: 106
Period size: 21 Copynumber: 4.0 Consensus size: 22
274873 CCTGTTTGTA
274883 AATAATAATTATTTAATAATAAT
1 AATAATAA-TATTTAATAATAAT
274906 -ATAAT-ATA--T-ATAAT-AT
1 AATAATAATATTTAATAATAAT
274922 AATAATAATATTTAATAATAAT
1 AATAATAATATTTAATAATAAT
274944 AATAATAAT-TTTAATAATAAT
1 AATAATAATATTTAATAATAAT
274965 TTAAGTAAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 14
0.79 0.00 0.21
Matches are distributed among these distances:
16 2 0.04
17 10 0.19
18 4 0.08
20 3 0.06
21 18 0.34
22 16 0.30
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
AATAATAATATTTAATAATAAT
Found at i:276271 original size:2 final size:2
Alignment explanation
Indices: 276266--276291 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
276256 TGAATCATGC
276266 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
276292 GAATGATCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:283621 original size:41 final size:41
Alignment explanation
Indices: 283576--283699 Score: 239
Period size: 41 Copynumber: 3.0 Consensus size: 41
283566 TTAATAAGGC
*
283576 CATAAGAGGATCAATCCAACCAAATTTAAAAACCTTTTTCA
1 CATAAGAGGATCAATCCAACCATATTTAAAAACCTTTTTCA
283617 CATAAGAGGATCAATCCAACCATATTTAAAAACCTTTTTCA
1 CATAAGAGGATCAATCCAACCATATTTAAAAACCTTTTTCA
283658 CATAAGAGGATCAATCCAACCATATTTAAAAACCTTTTTCA
1 CATAAGAGGATCAATCCAACCATATTTAAAAACCTTTTTCA
283699 C
1 C
283700 CATATTTCAA
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
41 82 1.00
ACGTcount: A:0.42, C:0.23, G:0.07, T:0.28
Consensus pattern (41 bp):
CATAAGAGGATCAATCCAACCATATTTAAAAACCTTTTTCA
Found at i:285819 original size:16 final size:16
Alignment explanation
Indices: 285772--285821 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 16
285762 TGCACTGTTA
* *
285772 TACATGAGCAATGTGT
1 TACATGATCTATGTGT
285788 TACATGTTATTCTATGTGT
1 TACATG--A-TCTATGTGT
285807 TACATGATCTATGTG
1 TACATGATCTATGTG
285822 AATATATGAG
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
16 14 0.48
17 1 0.03
18 1 0.03
19 13 0.45
ACGTcount: A:0.26, C:0.12, G:0.20, T:0.42
Consensus pattern (16 bp):
TACATGATCTATGTGT
Found at i:286069 original size:23 final size:23
Alignment explanation
Indices: 286033--286095 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
286023 GAGTCGAAGG
*
286033 TTCTACGCGGTCCTTCTGGACAA
1 TTCTACGCGGTCCTTCGGGACAA
* * * *
286056 TTCTACGTGATCCTTCGGGATAT
1 TTCTACGCGGTCCTTCGGGACAA
286079 TTCTACGCGGTCCTTCG
1 TTCTACGCGGTCCTTCG
286096 AGATATCTAT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.14, C:0.29, G:0.22, T:0.35
Consensus pattern (23 bp):
TTCTACGCGGTCCTTCGGGACAA
Found at i:286111 original size:21 final size:22
Alignment explanation
Indices: 286041--286138 Score: 74
Period size: 23 Copynumber: 4.4 Consensus size: 22
286031 GGTTCTACGC
*
286041 GGTCCTTCTG-GACAATTCTACGT
1 GGTCCTTC-GAGAC-ATTCTATGT
* * * * *
286064 GATCCTTCGGGATATTTCTACGC
1 GGTCCTTCGAGACA-TTCTATGT
*
286087 GGTCCTTCGAGATA-TCTATGT
1 GGTCCTTCGAGACATTCTATGT
*
286108 GGTCCTTCAAGACATTCTATGT
1 GGTCCTTCGAGACATTCTATGT
*
286130 GGTACTTCG
1 GGTCCTTCG
286139 GTGCAATTTA
Statistics
Matches: 61, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
21 17 0.28
22 16 0.26
23 28 0.46
ACGTcount: A:0.18, C:0.23, G:0.22, T:0.36
Consensus pattern (22 bp):
GGTCCTTCGAGACATTCTATGT
Found at i:286129 original size:22 final size:21
Alignment explanation
Indices: 286087--286137 Score: 66
Period size: 22 Copynumber: 2.4 Consensus size: 21
286077 ATTTCTACGC
* *
286087 GGTCCTTCGAGATATCTATGT
1 GGTCCTTCAAGACATCTATGT
286108 GGTCCTTCAAGACATTCTATGT
1 GGTCCTTCAAGACA-TCTATGT
*
286130 GGTACTTC
1 GGTCCTTC
286138 GGTGCAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 12 0.46
22 14 0.54
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.37
Consensus pattern (21 bp):
GGTCCTTCAAGACATCTATGT
Found at i:300533 original size:2 final size:2
Alignment explanation
Indices: 300526--300576 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
300516 AAAAGCATGC
300526 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
300568 AT AT AT AT A
1 AT AT AT AT A
300577 CCATTTTATG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:300603 original size:11 final size:11
Alignment explanation
Indices: 300526--300603 Score: 50
Period size: 12 Copynumber: 6.8 Consensus size: 11
300516 AAAAGCATGC
*
300526 ATATATA-TAT
1 ATATATATTTT
*
300536 ATATATATATAT
1 ATATATAT-TTT
*
300548 ATATATATATAT
1 ATATATAT-TTT
*
300560 ATATATATATAT
1 ATATATAT-TTT
*
300572 ATATACCATTTT
1 ATATA-TATTTT
*
300584 ATGTATATTTT
1 ATATATATTTT
*
300595 ATATGTATT
1 ATATATATT
300604 ATTAACAAAC
Statistics
Matches: 59, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
10 7 0.12
11 12 0.20
12 38 0.64
13 2 0.03
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (11 bp):
ATATATATTTT
Found at i:301870 original size:57 final size:63
Alignment explanation
Indices: 301800--301919 Score: 155
Period size: 61 Copynumber: 2.0 Consensus size: 63
301790 TATTATTATG
301800 TATTCATTTTATTTATA-TGTTAC-A-T-ATATATATATATATATA-TATA-TTTATTTCTTAA
1 TATTCATTTTATTTATAGT-TTACAACTAATATATATATATATATAGTATATTTTATTTCTTAA
*
301858 TATT-ATTTTATTTTTAGTTTACAAGCTAATATATATATATATATATGTATATTTTATTTCTT
1 TATTCATTTTATTTATAGTTTACAA-CTAATATATATATATATATA-GTATATTTTATTTCTT
301920 TTTTACCTTT
Statistics
Matches: 53, Mismatches: 1, Indels: 10
0.83 0.02 0.16
Matches are distributed among these distances:
57 15 0.28
58 6 0.11
60 1 0.02
61 17 0.32
63 4 0.08
64 10 0.19
ACGTcount: A:0.34, C:0.05, G:0.03, T:0.57
Consensus pattern (63 bp):
TATTCATTTTATTTATAGTTTACAACTAATATATATATATATATAGTATATTTTATTTCTTAA
Found at i:301958 original size:13 final size:13
Alignment explanation
Indices: 301937--301966 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
301927 TTTTTTCACG
*
301937 TTTTGTTTATTTA
1 TTTTATTTATTTA
301950 TTTTATTTATTTA
1 TTTTATTTATTTA
301963 TTTT
1 TTTT
301967 TCTTTTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.80
Consensus pattern (13 bp):
TTTTATTTATTTA
Found at i:306025 original size:2 final size:2
Alignment explanation
Indices: 306018--306049 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
306008 ACATTATAAT
*
306018 TA TA TA TA TA TG TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
306050 CACAATATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:306219 original size:95 final size:95
Alignment explanation
Indices: 306053--306246 Score: 298
Period size: 95 Copynumber: 2.0 Consensus size: 95
306043 ATATATACAC
* * **
306053 AATATACAATAAAGCTTGAGCTGTCCCTCTAAAGCAATTAGTTAAACACCCTGGCTTTATGGATA
1 AATATACAATAAAGCATGAGCTGTCCATCTAAAGCAATTAGTTAAACACCCCAGCTTTATGGATA
*
306118 AGATTCAGCTAGCCTGATAAAGGTGATTAT
66 AGATTCAGCTAGCCAGATAAAGGTGATTAT
* * * *
306148 AATATACAATAAAGCATGAGTTGTCCATCTAGAGTAATTAGTTAAACGCCCCAGCTTTATGGATA
1 AATATACAATAAAGCATGAGCTGTCCATCTAAAGCAATTAGTTAAACACCCCAGCTTTATGGATA
*
306213 ATATTCAGCTAGCCAGATAAAGGTGATTAT
66 AGATTCAGCTAGCCAGATAAAGGTGATTAT
306243 AATA
1 AATA
306247 CTAAGATGTC
Statistics
Matches: 89, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
95 89 1.00
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Consensus pattern (95 bp):
AATATACAATAAAGCATGAGCTGTCCATCTAAAGCAATTAGTTAAACACCCCAGCTTTATGGATA
AGATTCAGCTAGCCAGATAAAGGTGATTAT
Found at i:307621 original size:37 final size:36
Alignment explanation
Indices: 307580--307720 Score: 167
Period size: 36 Copynumber: 3.9 Consensus size: 36
307570 ACAAGGGGTC
* **
307580 GTCTCGCTTGAGACTAATTT-ACTCAAAACAAAGTTTT
1 GTCTCTCTTGAGAC-AATTTCACTTGAAACAAA-TTTT
**
307617 GTCTCTCTTGAGACAATTTGTCTTGAAACAAATTTT
1 GTCTCTCTTGAGACAATTTCACTTGAAACAAATTTT
* * *
307653 GTCTCTCTTAAGACAGTTTCCCTTGAAACAAATTTT
1 GTCTCTCTTGAGACAATTTCACTTGAAACAAATTTT
* *
307689 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 GTCTCTCTTGAGACAATTTCACTTGAAACAAA
307721 ATCTTTGAAT
Statistics
Matches: 94, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
36 72 0.77
37 22 0.23
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.37
Consensus pattern (36 bp):
GTCTCTCTTGAGACAATTTCACTTGAAACAAATTTT
Found at i:307653 original size:36 final size:36
Alignment explanation
Indices: 307605--307894 Score: 308
Period size: 36 Copynumber: 8.2 Consensus size: 36
307595 AATTTACTCA
* **
307605 AAACAAAGTTTTGTCTCTCTTGAGACAATTTGTCTTG
1 AAACAAA-TTTTGTCTCTCTTGAGACAGTTTCCCTTG
*
307642 AAACAAATTTTGTCTCTCTTAAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
307678 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
* * * *
307714 AAACAAA------ATCT-TTGA-ATATGTTTTCCTTA
1 AAACAAATTTTGTCTCTCTTGAGACA-GTTTCCCTTG
* **
307743 AAACAAATTTCGTCTCTCTTGAGACAGTTTCTTTTGG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTT-G
* * * *
307780 AAATAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTA
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
* * **
307816 AAACAAATTTTGTCTCTATTAAGGTAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
* *
307852 AAACAAATTTTGTCTCGCTTGAGACAGTTTCCCTTA
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
307888 AAACAAA
1 AAACAAA
307895 ATCTTTGAAT
Statistics
Matches: 209, Mismatches: 34, Indels: 21
0.79 0.13 0.08
Matches are distributed among these distances:
28 2 0.01
29 19 0.09
30 3 0.01
35 3 0.01
36 142 0.68
37 40 0.19
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (36 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
Found at i:307809 original size:138 final size:138
Alignment explanation
Indices: 307604--307858 Score: 377
Period size: 138 Copynumber: 1.8 Consensus size: 138
307594 TAATTTACTC
* *
307604 AAAACAAAGTTTTGTCTCTCTTGAGACAATTTGTCTTGAAACAAATTTTGTCTCTCTTAAGACAG
1 AAAACAAAGTTTCGTCTCTCTTGAGACAATTTCTCTTGAAACAAATTTTGTCTCTCTTAAGACAG
* * *
307669 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATATG
66 TTTCCCTTAAAACAAATTTTGTCTCTATTAAGACAGTTTCCCTTGAAACAAAATCTTTGAATATG
307734 TTTTCCTT
131 TTTTCCTT
* * * * *
307742 AAAACAAA-TTTCGTCTCTCTTGAGACAGTTTCTTTTGGAAATAAGTTTTGTCTCTCTTGAGACA
1 AAAACAAAGTTTCGTCTCTCTTGAGACAATTTCTCTT-GAAACAAATTTTGTCTCTCTTAAGACA
* **
307806 GTTTCTCTTAAAACAAATTTTGTCTCTATTAAGGTAGTTTCCCTTGAAACAAA
65 GTTTCCCTTAAAACAAATTTTGTCTCTATTAAGACAGTTTCCCTTGAAACAAA
307859 TTTTGTCTCG
Statistics
Matches: 103, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
137 24 0.23
138 79 0.77
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (138 bp):
AAAACAAAGTTTCGTCTCTCTTGAGACAATTTCTCTTGAAACAAATTTTGTCTCTCTTAAGACAG
TTTCCCTTAAAACAAATTTTGTCTCTATTAAGACAGTTTCCCTTGAAACAAAATCTTTGAATATG
TTTTCCTT
Found at i:307875 original size:174 final size:174
Alignment explanation
Indices: 307610--308134 Score: 775
Period size: 174 Copynumber: 3.0 Consensus size: 174
307600 ACTCAAAACA
* * *
307610 AAGTTTTGTCTCTCTTGAGACAATTTGTCTTGAAACAAATTTTGTCTCTCTTAAGACAGTTTCCC
1 AAGTTTTGTCTCTCTTGAGACAGTTTCTCTTAAAACAAATTTTGTCTCTCTTAAGACAGTTTCCC
307675 TTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATATGTTTTCC
66 TTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATATGTTTTCC
* *
307740 TTAAAACAAATTTCGTCTCTCTTGAGACAGTTTCTTTTGGAAAT
131 TTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAAAT
* **
307784 AAGTTTTGTCTCTCTTGAGACAGTTTCTCTTAAAACAAATTTTGTCTCTATTAAGGTAGTTTCCC
1 AAGTTTTGTCTCTCTTGAGACAGTTTCTCTTAAAACAAATTTTGTCTCTCTTAAGACAGTTTCCC
* * *
307849 TTGAAACAAATTTTGTCTCGCTTGAGACAGTTTCCCTTAAAACAAAATCTTTGAATCTGTTTTCC
66 TTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATATGTTTTCC
* * *
307914 TTGAAATAAATTTCGTCTCCCTCGAGACAGTTTCTTTTGGAACT
131 TTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAAAT
* * * *
307958 AAGTTTTGTCTCTCTTGAGGCAGTTTCTCTTTAAACAAAATTTGTCTCTCTTGAGACAGTTTCCC
1 AAGTTTTGTCTCTCTTGAGACAGTTTCTCTTAAAACAAATTTTGTCTCTCTTAAGACAGTTTCCC
* * * ** *
308023 TTGAAACAAAGTTTTGCCTCTCTTGAGACAGTTTCTCTTGAAACACCAATCTTTGAATATAATTC
66 TTGAAACAAA-TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACA-AAATCTTTGAATATGTTTT
*
308088 CCTTGAAACAAAATTGT-GTCTCCCTTGAGACAGTTTCTCTT-GAAAT
129 CCTTGAAAC-AAATT-TCGTCTCCCTTGAGACAGTTTCTTTTGGAAAT
308134 A
1 A
308135 CAAAAAAAAA
Statistics
Matches: 313, Mismatches: 34, Indels: 6
0.89 0.10 0.02
Matches are distributed among these distances:
174 228 0.73
175 30 0.10
176 27 0.09
177 27 0.09
178 1 0.00
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.40
Consensus pattern (174 bp):
AAGTTTTGTCTCTCTTGAGACAGTTTCTCTTAAAACAAATTTTGTCTCTCTTAAGACAGTTTCCC
TTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATATGTTTTCC
TTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAAAT
Found at i:307965 original size:138 final size:137
Alignment explanation
Indices: 307779--308032 Score: 355
Period size: 138 Copynumber: 1.8 Consensus size: 137
307769 GTTTCTTTTG
* * * * *
307779 GAAATAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTAAAACAAATTTTGTCTCTATTAAGGTAGT
1 GAAATAAATTTCGTCTCCCTCGAGACAGTTTCTCTTAAAACAAATTTTGTCTCTATTAAGGCAGT
*
307844 TTCCCTTGAAACAAATTTTGTCTCGCTTGAGACAGTTTCCCTTAAAACAAAATCTTTGAATCTGT
66 TTCCCTTGAAACAAAATTTGTCTCGCTTGAGACAGTTTCCCTTAAAACAAAATCTTTGAATCTGT
307909 TTTCCTT
131 TTTCCTT
* ** * * *
307916 GAAATAAATTTCGTCTCCCTCGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGGCAG
1 GAAATAAATTTCGTCTCCCTCGAGACAGTTTCTCTTAAAAC-AAATTTTGTCTCTATTAAGGCAG
* * * *
307981 TTTCTCTTTAAACAAAATTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
65 TTTCCCTTGAAACAAAATTTGTCTCGCTTGAGACAGTTTCCCTTAAAACAAA
308033 GTTTTGCCTC
Statistics
Matches: 100, Mismatches: 16, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
137 34 0.34
138 66 0.66
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.39
Consensus pattern (137 bp):
GAAATAAATTTCGTCTCCCTCGAGACAGTTTCTCTTAAAACAAATTTTGTCTCTATTAAGGCAGT
TTCCCTTGAAACAAAATTTGTCTCGCTTGAGACAGTTTCCCTTAAAACAAAATCTTTGAATCTGT
TTTCCTT
Found at i:308006 original size:36 final size:37
Alignment explanation
Indices: 307923--308067 Score: 175
Period size: 37 Copynumber: 3.9 Consensus size: 37
307913 CTTGAAATAA
* * * * *
307923 ATTTCGTCTCCCTCGAGACAGTTTCTTTTGGAACTAAG
1 ATTT-GTCTCTCTTGAGACAGTTTCTCTTGAAACAAAG
* * *
307961 TTTTGTCTCTCTTGAGGCAGTTTCTCTTTAAACAAA-
1 ATTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAG
*
307997 ATTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAG
1 ATTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAG
* *
308034 TTTTGCCTCTCTTGAGACAGTTTCTCTTGAAACA
1 ATTTGTCTCTCTTGAGACAGTTTCTCTTGAAACA
308068 CCAATCTTTG
Statistics
Matches: 91, Mismatches: 15, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
36 32 0.35
37 56 0.62
38 3 0.03
ACGTcount: A:0.23, C:0.22, G:0.16, T:0.39
Consensus pattern (37 bp):
ATTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAG
Found at i:308047 original size:73 final size:74
Alignment explanation
Indices: 307909--308067 Score: 207
Period size: 73 Copynumber: 2.2 Consensus size: 74
307899 TTGAATCTGT
* ** * * *
307909 TTTC-CTTGAAA-TAAATTTCGTCTCCCTCGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTC
1 TTTCTCTTGAAACAAAATTTCGTCTCCCTCGAGACAGTTTCCCTTGAAACAAAGTTTTGCCTCTC
*
307972 TTGAGGCAG
66 TTGAGACAG
* * *
307981 TTTCTCTTTAAACAAAATTT-GTCTCTCTTGAGACAGTTTCCCTTGAAACAAAGTTTTGCCTCTC
1 TTTCTCTTGAAACAAAATTTCGTCTCCCTCGAGACAGTTTCCCTTGAAACAAAGTTTTGCCTCTC
308045 TTGAGACAG
66 TTGAGACAG
308054 TTTCTCTTGAAACA
1 TTTCTCTTGAAACA
308068 CCAATCTTTG
Statistics
Matches: 74, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
72 4 0.05
73 64 0.86
74 6 0.08
ACGTcount: A:0.24, C:0.21, G:0.15, T:0.40
Consensus pattern (74 bp):
TTTCTCTTGAAACAAAATTTCGTCTCCCTCGAGACAGTTTCCCTTGAAACAAAGTTTTGCCTCTC
TTGAGACAG
Found at i:308161 original size:35 final size:36
Alignment explanation
Indices: 308120--308211 Score: 150
Period size: 37 Copynumber: 2.6 Consensus size: 36
308110 CCTTGAGACA
* *
308120 GTTTCTCTTGAAATACAAAAAAAAA-CTTTGAAATT
1 GTTTCTCTTGAAACACAAAAAAAAACCTTTGAAAAT
308155 GTTTCTCTTGAAACACAAAAAAAAACCCTTTGAAAAT
1 GTTTCTCTTGAAACACAAAAAAAAA-CCTTTGAAAAT
308192 GTTTCTCTTGAAACACAAAA
1 GTTTCTCTTGAAACACAAAA
308212 CCTTCGAGTT
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
35 24 0.45
37 29 0.55
ACGTcount: A:0.45, C:0.16, G:0.09, T:0.30
Consensus pattern (36 bp):
GTTTCTCTTGAAACACAAAAAAAAACCTTTGAAAAT
Found at i:308371 original size:84 final size:84
Alignment explanation
Indices: 308203--308463 Score: 265
Period size: 84 Copynumber: 3.1 Consensus size: 84
308193 TTTCTCTTGA
* * * * * * *
308203 AACACAAA-ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCTTTTGCAACATAGCTCAC
1 AACA-AAAGACCTTCGAGTTAGACTACGCTCAGCTCAAAGGCACATCATTTGCAGCATAACTTAA
* * * *
308267 GTCAATAAGAGTTATTTGCC
65 GTCAAGAAGGGCTATCTGCC
308287 AACAAAAGACCTTC-AGGTTAGACTACGCTCAGCTCAAAGGCACATCATTTGCAGCATAACTTAA
1 AACAAAAGACCTTCGA-GTTAGACTACGCTCAGCTCAAAGGCACATCATTTGCAGCATAACTTAA
*
308351 GTCGAGAAGGGCTATCTGCC
65 GTCAAGAAGGGCTATCTGCC
* * * * * * * *
308371 AACCAAAGACCTTCGAGTTCGATTACACTTAGCTCAGAGGCAAATCAAATTTACAGCATAACTTA
1 AACAAAAGACCTTCGAGTTAGACTACGCTCAGCTCAAAGGCACATC--ATTTGCAGCATAACTTA
* *
308436 AGGCAAGAAGGGCTATCTGTC
64 AGTCAAGAAGGGCTATCTGCC
*
308457 AATAAAA
1 AACAAAA
308464 TTGTTAATTC
Statistics
Matches: 147, Mismatches: 25, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
83 4 0.03
84 103 0.70
85 1 0.01
86 39 0.27
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.23
Consensus pattern (84 bp):
AACAAAAGACCTTCGAGTTAGACTACGCTCAGCTCAAAGGCACATCATTTGCAGCATAACTTAAG
TCAAGAAGGGCTATCTGCC
Found at i:309914 original size:3 final size:3
Alignment explanation
Indices: 309899--309960 Score: 72
Period size: 3 Copynumber: 21.0 Consensus size: 3
309889 TATCCCGATT
* * * * *
309899 TTA TTA TTT TTA TTA TTA TTA TAA TAA TTA TAA TTA TAA TTA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
309946 TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA
309961 AATAATTTTA
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
2 2 0.04
3 48 0.96
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:311342 original size:27 final size:24
Alignment explanation
Indices: 311285--311379 Score: 77
Period size: 27 Copynumber: 3.8 Consensus size: 24
311275 ATTATTATTA
* * *
311285 TTATTATTATATATAT-TATTTGA
1 TTATTTTTATAAATATATATTTGT
*
311308 TTAATTTTATAAAGTAATAATATTTGT
1 TTATTTTTATAAA-T-AT-ATATTTGT
*
311335 TTATTTTTATTAATATATATTAT-T
1 TTATTTTTATAAATATATATT-TGT
*
311359 TTATTTTTAATATATATATAT
1 TTATTTTT-ATAAATATATAT
311380 ATATATTATT
Statistics
Matches: 58, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
23 10 0.17
24 15 0.26
25 15 0.26
26 1 0.02
27 17 0.29
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (24 bp):
TTATTTTTATAAATATATATTTGT
Found at i:311349 original size:23 final size:24
Alignment explanation
Indices: 311275--311391 Score: 85
Period size: 24 Copynumber: 4.5 Consensus size: 24
311265 TATATGTTTA
*
311275 ATTATTATTATTATTATT-ATATAT
1 ATTATT-TTATTTTTATTAATATAT
* *
311299 ATTATTTGATTAATTTTATAAAGTAATAAT
1 ATTA-TT--TTATTTTTATTAA-T-AT-AT
311329 ATT-TGTTTATTTTTATTAATATAT
1 ATTAT-TTTATTTTTATTAATATAT
*
311353 ATTATTTTATTTTTAATATATATAT
1 ATTATTTTATTTTTATTA-ATATAT
*
311378 ATATATATTATTTT
1 AT-TATTTTATTTT
311392 AAACATGTTT
Statistics
Matches: 76, Mismatches: 7, Indels: 18
0.75 0.07 0.18
Matches are distributed among these distances:
24 21 0.28
25 13 0.17
26 20 0.26
27 12 0.16
28 2 0.03
29 3 0.04
30 5 0.07
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (24 bp):
ATTATTTTATTTTTATTAATATAT
Found at i:311359 original size:19 final size:21
Alignment explanation
Indices: 311341--311389 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 21
311331 TTGTTTATTT
311341 TTATTAATATATATTATTTTA
1 TTATTAATATATATTATTTTA
* *
311362 TTTTTAATATATATATATATATA
1 TTATTAATATATAT-TAT-TTTA
311385 TTATT
1 TTATT
311390 TTAAACATGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 13 0.57
22 3 0.13
23 7 0.30
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
TTATTAATATATATTATTTTA
Found at i:311504 original size:24 final size:22
Alignment explanation
Indices: 311466--311513 Score: 69
Period size: 24 Copynumber: 2.1 Consensus size: 22
311456 ATTTTCTGAT
*
311466 ATTTTTTTAAATAAATATCTTA
1 ATTTTTTTAAATAAATATATTA
311488 ATTTTTTATAAATTAAATATATTA
1 ATTTTTT-TAAA-TAAATATATTA
311512 AT
1 AT
311514 CTATTTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 7 0.30
23 4 0.17
24 12 0.52
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (22 bp):
ATTTTTTTAAATAAATATATTA
Found at i:313870 original size:35 final size:34
Alignment explanation
Indices: 313815--313916 Score: 107
Period size: 35 Copynumber: 2.9 Consensus size: 34
313805 TGTTACATTC
*
313815 ACATATTTATATTTGCATTTACATTTTGCATTTTT
1 ACATTTTTATATTTGCATTTACATTTT-CATTTTT
* * *
313850 GCATTTTTATGTTTGTATTTACATTTTCATTTTT
1 ACATTTTTATATTTGCATTTACATTTTCATTTTT
** *
313884 ACATTTGCATCTTTGCATAATTACATTTT-ATTT
1 ACATTTTTATATTTGCAT--TTACATTTTCATTT
313917 CAAATTATTT
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
34 20 0.36
35 27 0.48
36 9 0.16
ACGTcount: A:0.24, C:0.12, G:0.07, T:0.58
Consensus pattern (34 bp):
ACATTTTTATATTTGCATTTACATTTTCATTTTT
Found at i:316674 original size:1 final size:1
Alignment explanation
Indices: 316663--316760 Score: 79
Period size: 1 Copynumber: 98.0 Consensus size: 1
316653 TGAAGAAAGG
* * * * ** ** *
316663 AAAAAAGAAAAAAGAAAAAAAGAAAAAAAGAAAAAAAAAAAAAGGAAAAAAGGAAAAAAAGAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * *
316728 AAGAAAAAAAAGAAAAAAAGAAAAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
316761 TTGAATCAAA
Statistics
Matches: 75, Mismatches: 22, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 75 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (1 bp):
A
Found at i:316674 original size:7 final size:7
Alignment explanation
Indices: 316662--316760 Score: 117
Period size: 7 Copynumber: 13.0 Consensus size: 7
316652 TTGAAGAAAG
316662 GAAAAAA
1 GAAAAAA
316669 GAAAAAA
1 GAAAAAA
316676 GAAAAAAA
1 G-AAAAAA
316684 GAAAAAAA
1 G-AAAAAA
316692 GAAAAAA
1 GAAAAAA
*
316699 AAAAAAA
1 GAAAAAA
316706 GGAAAAAA
1 -GAAAAAA
316714 GGAAAAAAA
1 -G-AAAAAA
316723 GAAAAAA
1 GAAAAAA
316730 GAAAAAAAA
1 G--AAAAAA
316739 GAAAAAAA
1 G-AAAAAA
316747 GAAAAAA
1 GAAAAAA
316754 GAAAAAA
1 GAAAAAA
316761 TTGAATCAAA
Statistics
Matches: 85, Mismatches: 2, Indels: 10
0.88 0.02 0.10
Matches are distributed among these distances:
7 40 0.47
8 32 0.38
9 13 0.15
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (7 bp):
GAAAAAA
Found at i:316674 original size:8 final size:8
Alignment explanation
Indices: 316658--316760 Score: 142
Period size: 8 Copynumber: 13.2 Consensus size: 8
316648 ATACTTGAAG
*
316658 AAAGGAAA
1 AAAGAAAA
316666 AAAG-AAA
1 AAAGAAAA
316673 AAAGAAAA
1 AAAGAAAA
316681 AAAGAAAA
1 AAAGAAAA
316689 AAAGAAAA
1 AAAGAAAA
316697 AAA-AAAA
1 AAAGAAAA
*
316704 AAGGAAAA
1 AAAGAAAA
*
316712 AAGGAAAA
1 AAAGAAAA
316720 AAAG-AAA
1 AAAGAAAA
316727 AAAGAAAAA
1 AAAG-AAAA
316736 AAAGAAAA
1 AAAGAAAA
316744 AAAG-AAA
1 AAAGAAAA
316751 AAAGAAAA
1 AAAGAAAA
316759 AA
1 AA
316761 TTGAATCAAA
Statistics
Matches: 88, Mismatches: 2, Indels: 10
0.88 0.02 0.10
Matches are distributed among these distances:
7 27 0.31
8 54 0.61
9 7 0.08
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (8 bp):
AAAGAAAA
Found at i:316705 original size:31 final size:31
Alignment explanation
Indices: 316658--316760 Score: 154
Period size: 31 Copynumber: 3.3 Consensus size: 31
316648 ATACTTGAAG
* *
316658 AAAGGAAAAAAGAAAAAAGAAAAAAAGAAAA
1 AAAGAAAAAAAAAAAAAAGAAAAAAAGAAAA
* *
316689 AAAGAAAAAAAAAAAAAGGAAAAAAGGAAAA
1 AAAGAAAAAAAAAAAAAAGAAAAAAAGAAAA
316720 AAAGAAAAAAGAAAAAAAAGAAAAAAAG-AAA
1 AAAGAAAAAA-AAAAAAAAGAAAAAAAGAAAA
316751 AAAGAAAAAA
1 AAAGAAAAAA
316761 TTGAATCAAA
Statistics
Matches: 65, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
31 50 0.77
32 15 0.23
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (31 bp):
AAAGAAAAAAAAAAAAAAGAAAAAAAGAAAA
Found at i:320864 original size:22 final size:22
Alignment explanation
Indices: 320836--320892 Score: 96
Period size: 22 Copynumber: 2.6 Consensus size: 22
320826 ACATCTACAT
*
320836 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCCC
320858 TCTTCAAAGATGATAGATTCCC
1 TCTTCAAAGATGATAGATTCCC
*
320880 TTTTCAAAGATGA
1 TCTTCAAAGATGA
320893 AGGCTTTATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATTCCC
Found at i:321477 original size:112 final size:113
Alignment explanation
Indices: 321264--321686 Score: 658
Period size: 112 Copynumber: 3.8 Consensus size: 113
321254 TGAATCCATT
* * * *
321264 ACTCAATGGATCAACATTTCC-GGTAGAGTTCATAATGAGAAGAACTCATTTGAAGAAGGAAGAA
1 ACTCGATGGATTAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAA
321328 GAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTTAATTCATC
66 GAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTTAATTCATC
* *
321376 ACTCGATGGATTAGCATTGCAAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGG-AGAA
1 ACTCGATGGATTAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAA
* * *
321440 AAAGTTCATAATGAGAAGAACTTGTTTAACATTTTGCTTTAATTCATC
66 GAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTTAATTCATC
321488 ACTCGATGGATTAACATTGCCAGGTAGAGTTCAT-ATGAGAAGAACTCATCTGAAGAAGGAAGAA
1 ACTCGATGGATTAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAA
*
321552 GAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATC
66 GAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTTAATTCATC
* * * * *
321600 ACTCGATGGATCAACCTTTCCAGAG-AAAGTTCATAATGAGAAGAACTTATCTGAAG-AGGAAGA
1 ACTCGATGGATTAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA
*
321663 AGAAGTTCATAATGAGAATAACTT
65 AGAAGTTCATAATGAGAAGAACTT
321687 ATCTGAAGAG
Statistics
Matches: 286, Mismatches: 21, Indels: 8
0.91 0.07 0.03
Matches are distributed among these distances:
111 25 0.09
112 203 0.71
113 58 0.20
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (113 bp):
ACTCGATGGATTAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAA
GAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTTAATTCATC
Found at i:321710 original size:37 final size:39
Alignment explanation
Indices: 321626--321723 Score: 173
Period size: 39 Copynumber: 2.6 Consensus size: 39
321616 TTTCCAGAGA
321626 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAG
1 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAG
*
321665 AAGTTCATAATGAGAATAACTTATCTGAAGA-G-AGAAG
1 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAG
321702 AAGTTCATAATGAGAAGAACTT
1 AAGTTCATAATGAGAAGAACTT
321724 GTTCAACCTT
Statistics
Matches: 57, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
37 26 0.46
38 1 0.02
39 30 0.53
ACGTcount: A:0.46, C:0.08, G:0.22, T:0.23
Consensus pattern (39 bp):
AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAG
Found at i:321718 original size:17 final size:17
Alignment explanation
Indices: 321660--321720 Score: 52
Period size: 17 Copynumber: 3.4 Consensus size: 17
321650 CTGAAGAGGA
321660 AGAAGAAGTTCATAATG
1 AGAAGAAGTTCATAATG
* * *
321677 AGAATAACTT-ATCTGAAGAG
1 AGAAGAAGTTCA--T-AA-TG
321697 AGAAGAAGTTCATAATG
1 AGAAGAAGTTCATAATG
321714 AGAAGAA
1 AGAAGAA
321721 CTTGTTCAAC
Statistics
Matches: 33, Mismatches: 6, Indels: 10
0.67 0.12 0.20
Matches are distributed among these distances:
16 1 0.03
17 16 0.48
18 3 0.09
19 3 0.09
20 9 0.27
21 1 0.03
ACGTcount: A:0.49, C:0.07, G:0.23, T:0.21
Consensus pattern (17 bp):
AGAAGAAGTTCATAATG
Found at i:321970 original size:17 final size:17
Alignment explanation
Indices: 321916--321972 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
321906 CAGCATTTCC
*
321916 AGAAGGAGTTCATAATG
1 AGAAGAAGTTCATAATG
* *
321933 AGAAGAA-CTCAT-CTG
1 AGAAGAAGTTCATAATG
321948 ACGAAGAAGTTCATAATG
1 A-GAAGAAGTTCATAATG
321966 AGAAGAA
1 AGAAGAA
321973 CATGTTCAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
15 3 0.09
16 10 0.31
17 16 0.50
18 3 0.09
ACGTcount: A:0.46, C:0.11, G:0.25, T:0.19
Consensus pattern (17 bp):
AGAAGAAGTTCATAATG
Found at i:322206 original size:3 final size:3
Alignment explanation
Indices: 322191--322255 Score: 69
Period size: 3 Copynumber: 22.0 Consensus size: 3
322181 TATCCCGATT
* * * * *
322191 TTA TTA TTT TTA TTA TTA TTA TTA TAA TAA TTA TAA TTA TAA TTA TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
322238 GTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA
322256 AATAATTTTA
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
2 1 0.02
3 50 0.98
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:323596 original size:27 final size:26
Alignment explanation
Indices: 323554--323681 Score: 110
Period size: 27 Copynumber: 5.1 Consensus size: 26
323544 ATATGTTTAA
*
323554 TATTTTAATT-AT-TAT-TATTATTT
1 TATTTTTATTAATATATATATTATTT
*
323577 TATTTTTATTAATATATATTATT-TGAT
1 TATTTTTATTAATATATA-TATTAT-TT
* * *
323604 TAATTTTATAAAGTA-ATAATATTTTTT
1 TATTTTTATTAA-TATAT-ATATTATTT
323631 TATTTTTATT-A-ATATATATTATTT
1 TATTTTTATTAATATATATATTATTT
*
323655 TATTTTTA-AAATATATATATTATTT
1 TATTTTTATTAATATATATATTATTT
323680 TA
1 TA
323682 AACATGTTTT
Statistics
Matches: 85, Mismatches: 9, Indels: 20
0.75 0.08 0.18
Matches are distributed among these distances:
23 9 0.11
24 20 0.24
25 20 0.24
26 2 0.02
27 30 0.35
28 4 0.05
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (26 bp):
TATTTTTATTAATATATATATTATTT
Found at i:323794 original size:24 final size:22
Alignment explanation
Indices: 323753--323800 Score: 60
Period size: 24 Copynumber: 2.1 Consensus size: 22
323743 CCATTTTCTG
*
323753 ATTTTTTTAAATAAATATCTTA
1 ATTTTTTTAAATAAATATATTA
*
323775 ATTTTTTATAAATTATATATATTA
1 ATTTTTT-TAAA-TAAATATATTA
323799 AT
1 AT
323801 CTATTTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 7 0.32
23 4 0.18
24 11 0.50
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (22 bp):
ATTTTTTTAAATAAATATATTA
Found at i:333446 original size:16 final size:16
Alignment explanation
Indices: 333425--333460 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
333415 AATTAGATTT
*
333425 AATTCAAAATTAAATG
1 AATTCAAAATTAAATA
333441 AATTCAAAATTAAATA
1 AATTCAAAATTAAATA
333457 AATT
1 AATT
333461 AACGAGAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.58, C:0.06, G:0.03, T:0.33
Consensus pattern (16 bp):
AATTCAAAATTAAATA
Found at i:333727 original size:44 final size:44
Alignment explanation
Indices: 333598--333838 Score: 198
Period size: 44 Copynumber: 5.6 Consensus size: 44
333588 GGGCCTCAAT
* * * *
333598 TAGAAAGTGAGATTAAAAAAACTTA-AGGATCTCGATTATAAAGT
1 TAGAAAGTGAGATTTAAAAAACTTAGAGG-CCTCAATTATAAAGG
* *
333642 TAAAAAAGTGAGA-TT-AAAAA-TTAGGGGCCTCAATTATAAAGG
1 T-AGAAAGTGAGATTTAAAAAACTTAGAGGCCTCAATTATAAAGG
* *
333684 TAGAAATTGAGATTTAAAAAACTTAGAGGCCTTAATTGA-AAAGG
1 TAGAAAGTGAGATTTAAAAAACTTAGAGGCCTCAATT-ATAAAGG
* * * *
333728 TAGAAAGTGAGATTGAAAAAAACTTA-AAGCTTCAA-TATAAAGT
1 TAGAAAGTGAGATT-TAAAAAACTTAGAGGCCTCAATTATAAAGG
* * *
333771 TA-AAAGTGAGATTT-CAAAA-TTAGGGGCCTCAATTATAAAAG
1 TAGAAAGTGAGATTTAAAAAACTTAGAGGCCTCAATTATAAAGG
* * * *
333812 TAAAAAAT-AGATTGAAAAAAATTAGAG
1 TAGAAAGTGAGATTTAAAAAACTTAGAG
333839 AATTCAATTT
Statistics
Matches: 157, Mismatches: 27, Indels: 27
0.74 0.13 0.13
Matches are distributed among these distances:
39 3 0.02
40 10 0.06
41 22 0.14
42 38 0.24
43 24 0.15
44 39 0.25
45 21 0.13
ACGTcount: A:0.49, C:0.07, G:0.19, T:0.26
Consensus pattern (44 bp):
TAGAAAGTGAGATTTAAAAAACTTAGAGGCCTCAATTATAAAGG
Found at i:333847 original size:43 final size:42
Alignment explanation
Indices: 333797--333920 Score: 115
Period size: 44 Copynumber: 2.9 Consensus size: 42
333787 AAATTAGGGG
333797 CCTCAATTATAAAAGTAAAAAATAGATTGAAAAAAATTAGAGAA
1 CCTCAATTATAAAAGTAAAAAATAGATTGAAAAAAATTA-A-AA
* * * * * *
333841 -TTCAATTTTAAAAATAAAAAGTTAGATTGAATAATATTAAAA
1 CCTCAATTATAAAAGTAAAAA-ATAGATTGAAAAAAATTAAAA
* * *
333883 CCTCAATTACAAAGGTGAAAAAATAAGATTTAAAAAAA
1 CCTCAATTATAAAAGT-AAAAAAT-AGATTGAAAAAAA
333921 ACTAATGAAT
Statistics
Matches: 61, Mismatches: 15, Indels: 8
0.73 0.18 0.10
Matches are distributed among these distances:
42 2 0.03
43 29 0.48
44 30 0.49
ACGTcount: A:0.57, C:0.06, G:0.10, T:0.27
Consensus pattern (42 bp):
CCTCAATTATAAAAGTAAAAAATAGATTGAAAAAAATTAAAA
Found at i:334269 original size:15 final size:17
Alignment explanation
Indices: 334249--334281 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
334239 CTGATTTTTT
334249 TTAAATT-CAAG-TAGA
1 TTAAATTGCAAGATAGA
334264 TTAAATTGCAAGATAGA
1 TTAAATTGCAAGATAGA
334281 T
1 T
334282 AAAAATACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 4 0.25
17 5 0.31
ACGTcount: A:0.45, C:0.06, G:0.15, T:0.33
Consensus pattern (17 bp):
TTAAATTGCAAGATAGA
Found at i:334334 original size:10 final size:9
Alignment explanation
Indices: 334319--334367 Score: 57
Period size: 9 Copynumber: 5.3 Consensus size: 9
334309 ACATACTAAT
334319 TTTTTTTGTA
1 TTTTTTTG-A
334329 TTTTTTCTGA
1 TTTTTT-TGA
334339 -TTTTTTGTA
1 TTTTTTTG-A
334348 TTTTTTTGA
1 TTTTTTTGA
334357 TTTTTTT-A
1 TTTTTTTGA
334365 TTT
1 TTT
334368 AAATCCAAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
8 6 0.17
9 14 0.39
10 14 0.39
11 2 0.06
ACGTcount: A:0.10, C:0.02, G:0.08, T:0.80
Consensus pattern (9 bp):
TTTTTTTGA
Found at i:334344 original size:19 final size:18
Alignment explanation
Indices: 334320--334367 Score: 80
Period size: 19 Copynumber: 2.7 Consensus size: 18
334310 CATACTAATT
334320 TTTTTTGTATTTTTTCTGA
1 TTTTTTGTATTTTTT-TGA
334339 TTTTTTGTATTTTTTTGA
1 TTTTTTGTATTTTTTTGA
334357 TTTTTT-TATTT
1 TTTTTTGTATTT
334368 AAATCCAAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.17
18 9 0.31
19 15 0.52
ACGTcount: A:0.10, C:0.02, G:0.08, T:0.79
Consensus pattern (18 bp):
TTTTTTGTATTTTTTTGA
Found at i:334427 original size:116 final size:115
Alignment explanation
Indices: 334224--334564 Score: 566
Period size: 112 Copynumber: 3.0 Consensus size: 115
334214 CTACATTTTT
* *
334224 TTTTTTGTTATTTTTCTGA-TTTTT-TTTAAATTCAAGTAGATTAAATTGCAAGATAGATAAAAA
1 TTTTTTG-TATTTTTTTGATTTTTTATTTAAATTCAAGTAGATTAAATTGCAAGATATAT-AAAA
334287 TACATTGAAATTAGATAAATAAACATACTAATTTTTTTTGTATTTTTTCTGA
64 TACATTGAAATTAGATAAATAAACATACTAATTTTTTTTGTATTTTTTCTGA
*
334339 TTTTTTGTATTTTTTTGATTTTTTTATTTAAATCCAAGTAGATTAAATTGCAAGATATATAAAAT
1 TTTTTTGTATTTTTTTGA-TTTTTTATTTAAATTCAAGTAGATTAAATTGCAAGATATATAAAAT
334404 ACATTGAAATTAGATAAATAAACATACT-A-TTTTTTTGTATTTTTTCTGA
65 ACATTGAAATTAGATAAATAAACATACTAATTTTTTTTGTATTTTTTCTGA
*
334453 -TTTTTGTAATTTTTTGATTTTTTATTTAAATTCAAGTAGATTAAATTGCAAGATATATAAAATA
1 TTTTTTGTATTTTTTTGATTTTTTATTTAAATTCAAGTAGATTAAATTGCAAGATATATAAAATA
334517 CATTGAAATTAGATAAATAAACATACTAATATTTTTTTGTAATTTTTT
66 CATTGAAATTAGATAAATAAACATACTAAT-TTTTTTTGT-ATTTTTT
334565 TTTTGTATTT
Statistics
Matches: 214, Mismatches: 5, Indels: 13
0.92 0.02 0.06
Matches are distributed among these distances:
112 73 0.34
113 17 0.08
114 30 0.14
115 17 0.08
116 45 0.21
117 32 0.15
ACGTcount: A:0.36, C:0.06, G:0.09, T:0.49
Consensus pattern (115 bp):
TTTTTTGTATTTTTTTGATTTTTTATTTAAATTCAAGTAGATTAAATTGCAAGATATATAAAATA
CATTGAAATTAGATAAATAAACATACTAATTTTTTTTGTATTTTTTCTGA
Found at i:334458 original size:18 final size:17
Alignment explanation
Indices: 334435--334479 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 17
334425 ACATACTATT
334435 TTTTTGTATTTTTTCTGA
1 TTTTTGTATTTTTT-TGA
*
334453 TTTTTGTAATTTTTTGA
1 TTTTTGTATTTTTTTGA
334470 TTTTT-TATTT
1 TTTTTGTATTT
334480 AAATTCAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 4 0.16
17 8 0.32
18 13 0.52
ACGTcount: A:0.13, C:0.02, G:0.09, T:0.76
Consensus pattern (17 bp):
TTTTTGTATTTTTTTGA
Found at i:343359 original size:31 final size:31
Alignment explanation
Indices: 343321--343384 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
343311 TTACGTCAGA
*
343321 GACCATATTGCAAACGAACTAAATGTTGAGG
1 GACCATATTGAAAACGAACTAAATGTTGAGG
* * *
343352 GACCATATTGAAAATGGACTAAATGTTGGGG
1 GACCATATTGAAAACGAACTAAATGTTGAGG
343383 GA
1 GA
343385 TTATATTACA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.38, C:0.12, G:0.27, T:0.23
Consensus pattern (31 bp):
GACCATATTGAAAACGAACTAAATGTTGAGG
Found at i:344928 original size:31 final size:31
Alignment explanation
Indices: 344893--344954 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
344883 ATATAATCCC
** *
344893 CAACATTTAGTCTGTTTGTAATATGGGCCCT
1 CAACATTTAGTCAATTTGCAATATGGGCCCT
*
344924 CAACATTTAGTCAATTTGCAATATGGTCCCT
1 CAACATTTAGTCAATTTGCAATATGGGCCCT
344955 GATATAACTG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (31 bp):
CAACATTTAGTCAATTTGCAATATGGGCCCT
Found at i:345029 original size:29 final size:29
Alignment explanation
Indices: 344997--345062 Score: 114
Period size: 29 Copynumber: 2.3 Consensus size: 29
344987 GACTAAATAT
*
344997 TGGGGGACTGTATTGCAAGTTTTAAATGC
1 TGGGGGACTGTATTGCAAGTTTTAAAAGC
*
345026 TGGGGGACTGTATTGCAAGTTTTAAAAGT
1 TGGGGGACTGTATTGCAAGTTTTAAAAGC
345055 TGGGGGAC
1 TGGGGGAC
345063 CTAAATGAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.24, C:0.09, G:0.35, T:0.32
Consensus pattern (29 bp):
TGGGGGACTGTATTGCAAGTTTTAAAAGC
Found at i:345558 original size:14 final size:14
Alignment explanation
Indices: 345539--345569 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
345529 TCCTTTCTCA
*
345539 TTTCCCTTATTTGC
1 TTTCCCTCATTTGC
345553 TTTCCCTCATTTGC
1 TTTCCCTCATTTGC
345567 TTT
1 TTT
345570 TCTTCAGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.06, C:0.29, G:0.06, T:0.58
Consensus pattern (14 bp):
TTTCCCTCATTTGC
Found at i:346465 original size:133 final size:133
Alignment explanation
Indices: 346219--346569 Score: 429
Period size: 133 Copynumber: 2.6 Consensus size: 133
346209 GTCAGAGGCA
* * ** * *
346219 GTTGACGTTGCTCCTACGTGATGCGGAGATATGGTTAGTGGATGACACGATTCTTACGTGATGAG
1 GTTGACGTGGCTCCTACGTGATGAGGAGATATGGTCGGTGGATGACACGGTTCCTACGTGATGAG
* * * * * *
346284 GATGACTGTCCATCTTTAAGGAGATGATAACACGGTTCTTACACGATGAAGAT-GACTGGTTATC
66 GACGGCTGACCATCTTTAGGGAGATGATAACACGGTTCATACACGATGAAGATAG-CTGGTTATA
346348 TAAG
130 TAAG
* * *
346352 GTTGACGCGGCTCCTACGTTATGAGGAGATTTGGTCGGTGGATGACACGGTTCCTACGTGATGAG
1 GTTGACGTGGCTCCTACGTGATGAGGAGATATGGTCGGTGGATGACACGGTTCCTACGTGATGAG
* ** *
346417 GACGGCT-ACCATATTTAGGGATGATGATAACACGGTTCATACGTGATGAGGATAGCTGGTTATA
66 GACGGCTGACCATCTTTAGGGA-GATGATAACACGGTTCATACACGATGAAGATAGCTGGTTATA
346481 TAAG
130 TAAG
* * * * * *
346485 GGTGACGTGGTTCCTACGTGATGTGGAGATCTGGTCGGTGGATGACACAGTTCCTACGCGATGAG
1 GTTGACGTGGCTCCTACGTGATGAGGAGATATGGTCGGTGGATGACACGGTTCCTACGTGATGAG
346550 GACAGG-TGACCATCTTTAGG
66 GAC-GGCTGACCATCTTTAGG
346570 AATAAATTGT
Statistics
Matches: 186, Mismatches: 28, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
132 11 0.06
133 161 0.87
134 14 0.08
ACGTcount: A:0.24, C:0.17, G:0.31, T:0.28
Consensus pattern (133 bp):
GTTGACGTGGCTCCTACGTGATGAGGAGATATGGTCGGTGGATGACACGGTTCCTACGTGATGAG
GACGGCTGACCATCTTTAGGGAGATGATAACACGGTTCATACACGATGAAGATAGCTGGTTATAT
AAG
Found at i:346632 original size:36 final size:36
Alignment explanation
Indices: 346573--346707 Score: 166
Period size: 36 Copynumber: 3.8 Consensus size: 36
346563 CTTTAGGAAT
* *
346573 AAAT-TGTTTCAAGAGAAACTGTCTCAAAAGAGACA
1 AAATATGTTTCAAGGGAAACTGTCTCAAGAGAGACA
* * * *
346608 ACACATGTATCAAGGGAAATTGTCTCAAGAGAGACA
1 AAATATGTTTCAAGGGAAACTGTCTCAAGAGAGACA
**
346644 AAATATGTTTCAACGGG-AACAATCTCAAGAGAGACA
1 AAATATGTTTCAA-GGGAAACTGTCTCAAGAGAGACA
*
346680 AAATATGTTTCAAGGGAAACAGTCTCAA
1 AAATATGTTTCAAGGGAAACTGTCTCAA
346708 TGTTTTTATT
Statistics
Matches: 84, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
35 5 0.06
36 76 0.90
37 3 0.04
ACGTcount: A:0.44, C:0.16, G:0.19, T:0.21
Consensus pattern (36 bp):
AAATATGTTTCAAGGGAAACTGTCTCAAGAGAGACA
Found at i:346946 original size:37 final size:36
Alignment explanation
Indices: 346854--346956 Score: 118
Period size: 37 Copynumber: 2.8 Consensus size: 36
346844 GACGGGATTT
* *
346854 GTTTTTAGAGAAATTATCTCAAGCGAGACAAAATTT
1 GTTTTTAGAGAAATTGTCTCAAGCGAGACAAAATTG
* * *
346890 GTTTTTAGATAAAACTGTCTCAAGAGAGACAAAATTG
1 GTTTTTAGA-GAAATTGTCTCAAGCGAGACAAAATTG
*
346927 GTTTTTTAGA-AAATTTGTCTCTAGCGAGAC
1 G-TTTTTAGAGAAA-TTGTCTCAAGCGAGAC
346957 GACACTTTGT
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
36 12 0.21
37 36 0.64
38 8 0.14
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.34
Consensus pattern (36 bp):
GTTTTTAGAGAAATTGTCTCAAGCGAGACAAAATTG
Found at i:350346 original size:23 final size:21
Alignment explanation
Indices: 350320--350361 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
350310 CAATACATGT
*
350320 AGTATTATATATATATATAATAA
1 AGTAATATATA-ATA-ATAATAA
350343 AGTAATATATAATAATAAT
1 AGTAATATATAATAATAAT
350362 GTACGTGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 3 0.17
23 10 0.56
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (21 bp):
AGTAATATATAATAATAATAA
Found at i:352052 original size:41 final size:41
Alignment explanation
Indices: 352007--352084 Score: 95
Period size: 41 Copynumber: 1.9 Consensus size: 41
351997 TTGAAAACAC
* *
352007 CTTGCCCGAAGGTCTTATTGATGGCCC-AAATGACTTATCGT
1 CTTGCCCGAAAGTCTTATAGATGGCCCGAAA-GACTTATCGT
***
352048 CTTGCTTTAAAGTCTTATAGATGGCCCGAAAGACTTA
1 CTTGCCCGAAAGTCTTATAGATGGCCCGAAAGACTTA
352085 CACATCATAC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
41 28 0.90
42 3 0.10
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.32
Consensus pattern (41 bp):
CTTGCCCGAAAGTCTTATAGATGGCCCGAAAGACTTATCGT
Found at i:352374 original size:144 final size:145
Alignment explanation
Indices: 352113--352415 Score: 475
Period size: 144 Copynumber: 2.1 Consensus size: 145
352103 CTTACTGATA
* *
352113 GCCCGAAGGACTTCATCTGATTCGAAGTGCTATGAATCGAGCAACAGGAAATGTTAACCCCTCTG
1 GCCCGAAGGACTTAAGCTGATTCGAAGTGCTATGAATCGAGCAACAGGAAATGTTAACCCCTCTG
* * *
352178 GCGGGGCGTTTCTGATTCGAAGTGTTGTGAATCGAGCAAAGAAAATGTTGAAAACATTC-TGCCC
66 GCGGGGCATTGCTGATTCGAAGTGTTGTGAATCAAGCAAAGAAAATGTTGAAAACA-TCATGCCC
352242 GAAGGTCTTATGGAAG
130 GAAGGTCTTATGGAAG
* * **
352258 GCCCGAAGGACTTAAGCTGATTCTAAGTG-TGTGAATCGAGCAATGGGAAATGTTAACCCCTCTG
1 GCCCGAAGGACTTAAGCTGATTCGAAGTGCTATGAATCGAGCAACAGGAAATGTTAACCCCTCTG
* *
352322 GTGGGGCATTGCTGATTCGAAGTGTTGTGAATCAAGCAAAGGAAATGTTGAAAACATCATGCCCG
66 GCGGGGCATTGCTGATTCGAAGTGTTGTGAATCAAGCAAAGAAAATGTTGAAAACATCATGCCCG
*
352387 AAGGTCTTATGGATG
131 AAGGTCTTATGGAAG
352402 GCCCGAAGGACTTA
1 GCCCGAAGGACTTA
352416 TCATCTTGCT
Statistics
Matches: 145, Mismatches: 12, Indels: 3
0.91 0.08 0.02
Matches are distributed among these distances:
143 2 0.01
144 117 0.81
145 26 0.18
ACGTcount: A:0.29, C:0.18, G:0.28, T:0.25
Consensus pattern (145 bp):
GCCCGAAGGACTTAAGCTGATTCGAAGTGCTATGAATCGAGCAACAGGAAATGTTAACCCCTCTG
GCGGGGCATTGCTGATTCGAAGTGTTGTGAATCAAGCAAAGAAAATGTTGAAAACATCATGCCCG
AAGGTCTTATGGAAG
Found at i:352437 original size:41 final size:41
Alignment explanation
Indices: 352392--352503 Score: 111
Period size: 42 Copynumber: 2.7 Consensus size: 41
352382 GCCCGAAGGT
**
352392 CTTATGGATGGCCCGAAGGACTTA-TCATCTTGCTCGAAAGA
1 CTTAT-GATGGCCCGAAGGACTTACTCATCACGCTCGAAAGA
* * *
352433 CTTATAGATGACCCGAAGGATTTAAGT-ATCACGCTCGAAAGA
1 CTTAT-GATGGCCCGAAGGACTT-ACTCATCACGCTCGAAAGA
* *
352475 CTTACTGATGGCCCCAAAGACTTACTCAT
1 CTTA-TGATGGCCCGAAGGACTTACTCAT
352504 TAAGAAACCC
Statistics
Matches: 57, Mismatches: 10, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
41 22 0.39
42 33 0.58
43 2 0.04
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (41 bp):
CTTATGATGGCCCGAAGGACTTACTCATCACGCTCGAAAGA
Found at i:352753 original size:52 final size:52
Alignment explanation
Indices: 352640--352768 Score: 161
Period size: 52 Copynumber: 2.5 Consensus size: 52
352630 TTATAAAAAC
* *
352640 TCATTTGAAAATATCAAGAAATCCCTAAAAAATAGGCTTAACTTCTTTGAAAT
1 TCATTTGAAAACATCAAGAAA-CCCTAAAAAATAGGCTTAACTTCTTTCAAAT
* * * * *
352693 TCACTTGAAAACATTAAGAAACCC-ATAAAATTAGTCTTAGCTTCTTTCAAAT
1 TCATTTGAAAACATCAAGAAACCCTA-AAAAATAGGCTTAACTTCTTTCAAAT
*
352745 TCATTTGAAAACATCGAGAAACCC
1 TCATTTGAAAACATCAAGAAACCC
352769 CTGAAAATCA
Statistics
Matches: 65, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
51 1 0.02
52 46 0.71
53 18 0.28
ACGTcount: A:0.42, C:0.19, G:0.09, T:0.30
Consensus pattern (52 bp):
TCATTTGAAAACATCAAGAAACCCTAAAAAATAGGCTTAACTTCTTTCAAAT
Found at i:352845 original size:38 final size:38
Alignment explanation
Indices: 352792--352872 Score: 126
Period size: 38 Copynumber: 2.1 Consensus size: 38
352782 TTAGTTTCTA
* * * *
352792 AAAATCTTTTTTTTGAGTGAAACTATCTCTAGCGAGAT
1 AAAATCTTCTATTTGAGGGAAACTATCTCAAGCGAGAT
352830 AAAATCTTCTATTTGAGGGAAACTATCTCAAGCGAGAT
1 AAAATCTTCTATTTGAGGGAAACTATCTCAAGCGAGAT
352868 AAAAT
1 AAAAT
352873 TTGGTTTTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (38 bp):
AAAATCTTCTATTTGAGGGAAACTATCTCAAGCGAGAT
Found at i:352947 original size:40 final size:39
Alignment explanation
Indices: 352849--352965 Score: 109
Period size: 37 Copynumber: 3.1 Consensus size: 39
352839 TATTTGAGGG
352849 AAACTATCTCAAGCGAGAT-AA-AATTTGGTTTTAAGAA
1 AAACTATCTCAAGCGAGATGAATAATTTGGTTTTAAGAA
* ** * * * * *
352886 AAACAATCTTGAGTGAAATGAATATTTTTGTTTTAGGTAA
1 AAACTATCTCAAGCGAGATGAATAATTTGGTTTTAAG-AA
*
352926 AAACTATCTCAAGCGAGATGAAT--CTT-GTTTTAAGAA
1 AAACTATCTCAAGCGAGATGAATAATTTGGTTTTAAGAA
352962 AAAC
1 AAAC
352966 AATATGTAGT
Statistics
Matches: 62, Mismatches: 15, Indels: 7
0.74 0.18 0.08
Matches are distributed among these distances:
36 6 0.10
37 21 0.34
38 4 0.06
39 11 0.18
40 20 0.32
ACGTcount: A:0.41, C:0.10, G:0.16, T:0.32
Consensus pattern (39 bp):
AAACTATCTCAAGCGAGATGAATAATTTGGTTTTAAGAA
Found at i:352977 original size:76 final size:76
Alignment explanation
Indices: 352849--353414 Score: 693
Period size: 76 Copynumber: 7.4 Consensus size: 76
352839 TATTTGAGGG
* *
352849 AAACTATCTCAAGCGAGATAAAAT-TTGGTTTTAAGAAAAACAATCTTGAGTGAAATGAATAT-T
1 AAACTGTCTCAAGCGAGA-CAAATCTT-GTTTTAAGAAAAACAATCTTGAGTGAAATGAA-ATGT
*
352912 TTTGTTTTAG-GTAA
63 TTT-TTTTAGAGCAA
* ** * **
352926 AAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAAAAACAAT-ATGTAGTGAAACAAAATGTCT
1 AAACTGTCTCAAGCGAGACAAATCTTGTTTTAAGAAAAACAATCTTG-AGTGAAATGAAATGT-T
* *
352990 TGTTTT-GAGTAA
64 TTTTTTAGAGCAA
* * * *
353002 AAAATGTCTCAAGCGACACAAATTTTGTTTTAAGAAAAACAATCTTGAGTGAAATGAAATGTATT
1 AAACTGTCTCAAGCGAGACAAATCTTGTTTTAAGAAAAACAATCTTGAGTGAAATGAAATGTTTT
*
353067 TTTTCGAGCAA
66 TTTTAGAGCAA
* *
353078 AAACTGTCTCAAGTGAGATAAATCTTGTTTTAAGAAAAACAATCTTGAGTGAAATGAAATGCATT
1 AAACTGTCTCAAGCGAGACAAATCTTGTTTTAAGAAAAACAATCTTGAGTGAAATGAAATG--TT
*
353143 TTTTCT-GAGCAA
64 TTTTTTAGAGCAA
** * *
353155 AATTTGTCTCAAGCGAGACAAATCTTGTTTTAAGAAAAACAATCTTGAGTAAAATGAAATGTATT
1 AAACTGTCTCAAGCGAGACAAATCTTGTTTTAAGAAAAACAATCTTGAGTGAAATGAAATGTTTT
353220 TTTT-GAGCAA
66 TTTTAGAGCAA
* *
353230 AAACTATCTCAAGCGAGACAAATCTTGTTTTAAGAAAAACAATCTTGAGTAAAATGAAATGTATT
1 AAACTGTCTCAAGCGAGACAAATCTTGTTTTAAGAAAAACAATCTTGAGTGAAATGAAATGT-TT
*
353295 TTTTT-TAGCAA
65 TTTTTAGAGCAA
*
353306 AAACTGTCTCAAGCGAGACAAATCTTGTTTTAAGAAAAACAATCTTGAGTGAAATAAAATGTATT
1 AAACTGTCTCAAGCGAGACAAATCTTGTTTTAAGAAAAACAATCTTGAGTGAAATGAAATGT-TT
* **
353371 CTTTT-GAATAA
65 TTTTTAGAGCAA
*
353382 AAA-TGTCTCAAGCGAGACAAATCTTGTATTAAG
1 AAACTGTCTCAAGCGAGACAAATCTTGTTTTAAG
353415 GGAAACAAAT
Statistics
Matches: 434, Mismatches: 45, Indels: 22
0.87 0.09 0.04
Matches are distributed among these distances:
75 110 0.25
76 232 0.53
77 86 0.20
78 6 0.01
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.32
Consensus pattern (76 bp):
AAACTGTCTCAAGCGAGACAAATCTTGTTTTAAGAAAAACAATCTTGAGTGAAATGAAATGTTTT
TTTTAGAGCAA
Found at i:353260 original size:228 final size:226
Alignment explanation
Indices: 352849--353414 Score: 764
Period size: 228 Copynumber: 2.5 Consensus size: 226
352839 TATTTGAGGG
*
352849 AAACTATCTCAAGCGAGATAAAAT-TTGGTTTTAAGAAAAACAATCTTGAGTGAAATG-AAT-AT
1 AAACTGTCTCAAGCGAGAT-AAATCTT-GTTTTAAGAAAAACAATCTTGAGTGAAATGAAATGA-
* * **
352911 TTTTGTTTTAGGTAAAAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAAAAACAATATGTAGT
63 TTTT-TTTGA-GTAAAAA-TGTCTCAAGCGAGACAAATCTTGTTTTAAGAAAAACAATATGTAGT
* * * * *
352976 GAAACAAAATGTCTTGTTTTGAGTAAAAAATGTCTCAAGCGACACAAATTTTGTTTTAAGAAAAA
125 AAAACAAAATGTATTGTTTTGAGCAAAAAATATCTCAAGCGACACAAATCTTGTTTTAAGAAAAA
*
353041 CAATCTTGAGTGAAATGAAATGTATTTTTTCGAGCAA
190 CAATCTTGAGTAAAATGAAATGTATTTTTTCGAGCAA
*
353078 AAACTGTCTCAAGTGAGATAAATCTTGTTTTAAGAAAAACAATCTTGAGTGAAATGAAATGCATT
1 AAACTGTCTCAAGCGAGATAAATCTTGTTTTAAGAAAAACAATCTTGAGTGAAATGAAATG-ATT
* * *
353143 TTTTCTGAGCAAAATTTGTCTCAAGCGAGACAAATCTTGTTTTAAGAAAAACAATCT-TGAGTAA
65 TTTT-TGAGTAAAA-ATGTCTCAAGCGAGACAAATCTTGTTTTAAGAAAAACAATATGT-AGTAA
** * *
353207 AATGAAATGTATT-TTTTGAGCAAAAACTATCTCAAGCGAGACAAATCTTGTTTTAAGAAAAACA
127 AACAAAATGTATTGTTTTGAGCAAAAAATATCTCAAGCGACACAAATCTTGTTTTAAGAAAAACA
**
353271 ATCTTGAGTAAAATGAAATGTATTTTTTTTAGCAA
192 ATCTTGAGTAAAATGAAATGTATTTTTTCGAGCAA
* *
353306 AAACTGTCTCAAGCGAGACAAATCTTGTTTTAAGAAAAACAATCTTGAGTGAAATAAAATGTATT
1 AAACTGTCTCAAGCGAGATAAATCTTGTTTTAAGAAAAACAATCTTGAGTGAAATGAAATG-ATT
* * *
353371 CTTTTGAATAAAAATGTCTCAAGCGAGACAAATCTTGTATTAAG
65 TTTTTGAGTAAAAATGTCTCAAGCGAGACAAATCTTGTTTTAAG
353415 GGAAACAAAT
Statistics
Matches: 300, Mismatches: 30, Indels: 17
0.86 0.09 0.05
Matches are distributed among these distances:
226 29 0.10
227 7 0.02
228 177 0.59
229 80 0.27
230 6 0.02
231 1 0.00
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.32
Consensus pattern (226 bp):
AAACTGTCTCAAGCGAGATAAATCTTGTTTTAAGAAAAACAATCTTGAGTGAAATGAAATGATTT
TTTTGAGTAAAAATGTCTCAAGCGAGACAAATCTTGTTTTAAGAAAAACAATATGTAGTAAAACA
AAATGTATTGTTTTGAGCAAAAAATATCTCAAGCGACACAAATCTTGTTTTAAGAAAAACAATCT
TGAGTAAAATGAAATGTATTTTTTCGAGCAA
Found at i:353455 original size:15 final size:15
Alignment explanation
Indices: 353437--353488 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
353427 AAAGATTTTG
353437 TGTTTCAAGAGAAAC
1 TGTTTCAAGAGAAAC
*
353452 TGTTTCAAGGGAGACAAAA
1 TGTTTCAA--GAG--AAAC
*
353471 TTTTTCAAGAGAAAC
1 TGTTTCAAGAGAAAC
353486 TGT
1 TGT
353489 CTAAAGGGAG
Statistics
Matches: 29, Mismatches: 4, Indels: 8
0.71 0.10 0.20
Matches are distributed among these distances:
15 13 0.45
17 6 0.21
19 10 0.34
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (15 bp):
TGTTTCAAGAGAAAC
Found at i:353523 original size:37 final size:36
Alignment explanation
Indices: 353437--353585 Score: 212
Period size: 37 Copynumber: 4.1 Consensus size: 36
353427 AAAGATTTTG
*
353437 TGTTTCAAGAGAAACTGTTTCAAGGGAGACAAAA-T
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT
*
353472 T-TTTCAAGAGAAACTGTCTAAAGGGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TT
* * *
353508 TGTTTCAAGATAAACTATCTCAAGGGAGACAGAATTT
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACA-AAATT
*
353545 TGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT
353581 TGTTT
1 TGTTT
353586 GGATTGTCTC
Statistics
Matches: 100, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
34 30 0.30
35 1 0.01
36 11 0.11
37 56 0.56
38 2 0.02
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT
Found at i:353594 original size:30 final size:30
Alignment explanation
Indices: 353558--353614 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
353548 TTCAAGAGAA
353558 ATTGTCTCAAGGGAGACAAAATTTGTTTGG
1 ATTGTCTCAAGGGAGACAAAATTTGTTTGG
*
353588 ATTGTCTCAAGTGAGACAAAATTTGTT
1 ATTGTCTCAAGGGAGACAAAATTTGTT
353615 CTTTGGAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.32, C:0.11, G:0.23, T:0.35
Consensus pattern (30 bp):
ATTGTCTCAAGGGAGACAAAATTTGTTTGG
Found at i:353745 original size:36 final size:36
Alignment explanation
Indices: 353679--353939 Score: 177
Period size: 36 Copynumber: 7.1 Consensus size: 36
353669 TGGGAGAATG
* ** * * *
353679 TCTCAAGCGAGACGATGTTTGTTTTGAGAGAAAGTG
1 TCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAATA
* *
353715 TCTCAAGTGAGACAAAATTTATTTTTAGAGAAAACTA
1 TCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAA-TA
* * *
353752 TCTCAAGCAAGATAAAATTTGTTTTTGGAGAAAATAA
1 TCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAAT-A
* ** * * *
353789 TCTCAAGTGAGATTAATTTTGTTTTAAG-GAAAACTG
1 TCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAA-TA
*
353825 TCTCAAGCGAGACAAAATTTGTTTTTTGGAGAAAATAA
1 TCTCAAGCGAGACAAAATTTG-TTTTTAGAGAAAAT-A
* ** * * *
353863 TCTCAAGTGAGATTAATTTTGTTTTAAG-GAAAATTG
1 TCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAA-TA
* * ** *
353899 TCTCCAGTGATTCAAAATTTGTTCTTAG-GAAAATTA
1 TCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAA-TA
353935 TCTCA
1 TCTCA
353940 TGTGAGATCA
Statistics
Matches: 174, Mismatches: 44, Indels: 14
0.75 0.19 0.06
Matches are distributed among these distances:
36 86 0.49
37 66 0.38
38 22 0.13
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.35
Consensus pattern (36 bp):
TCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAATA
Found at i:353860 original size:74 final size:73
Alignment explanation
Indices: 353677--353959 Score: 311
Period size: 74 Copynumber: 3.9 Consensus size: 73
353667 TTTGGGAGAA
* ** * * ** * *
353677 TGTCTCAAGCGAGACGATGTTTG-TTTTGAGAGAAAGT-GTCTCAAGTGAGACAAAATTTATTTT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTG-GAGAAAATAATCTCAAGTGAGATTAATTTTGTTTT
*
353740 TAGAGAAAAC
65 AAG-GAAAAC
* * *
353750 TATCTCAAGCAAGATAAAATTTGTTTTTGGAGAAAATAATCTCAAGTGAGATTAATTTTGTTTTA
1 TGTCTCAAGCGAGACAAAATTTGTTTTTGGAGAAAATAATCTCAAGTGAGATTAATTTTGTTTTA
353815 AGGAAAAC
66 AGGAAAAC
353823 TGTCTCAAGCGAGACAAAATTTGTTTTTTGGAGAAAATAATCTCAAGTGAGATTAATTTTGTTTT
1 TGTCTCAAGCGAGACAAAATTTG-TTTTTGGAGAAAATAATCTCAAGTGAGATTAATTTTGTTTT
*
353888 AAGGAAAAT
65 AAGGAAAAC
* * ** * * * * *
353897 TGTCTCCAGTGATTCAAAATTTGTTCTTAG-GAAAATTATCTCATGTGAGATCAATTTTGTTTT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTGGAGAAAATAATCTCAAGTGAGATTAATTTTGTTTT
353960 TTTTGTGTGA
Statistics
Matches: 181, Mismatches: 26, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
72 30 0.17
73 55 0.30
74 96 0.53
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.37
Consensus pattern (73 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTTGGAGAAAATAATCTCAAGTGAGATTAATTTTGTTTTA
AGGAAAAC
Found at i:353939 original size:110 final size:110
Alignment explanation
Indices: 353715--353961 Score: 245
Period size: 110 Copynumber: 2.2 Consensus size: 110
353705 AGAGAAAGTG
* **
353715 TCTCAAGTGAGACAAAATTT-ATTTTTAGAGAAAACTATCTCAAGCAAGATAAAATTTGTTTTTG
1 TCTCAAGTGAGACAAAATTTGTTTTTTAGAGAAAACTATCTCAAGCAAGATAAAATTTGTTTTAA
* *
353779 GAGAAAATAATCTCAAGTGAGATTAATTTTGTTTTAAGGAAAACTG
66 GAGAAAATAATCTCAAGT-AGATTAAATTTGTTTTAAGGAAAACTA
* * ** * *
353825 TCTCAAGCGAGACAAAATTTGTTTTTTGGAGAAAA-TAATCTCAAGTGAGATTAATTTTGTTTTA
1 TCTCAAGTGAGACAAAATTTGTTTTTTAGAGAAAACT-ATCTCAAGCAAGATAAAATTTGTTTTA
** * *
353889 AG-GAAAATTGTCTCCAGT-GATTCAAAATTTGTTCTT-AGGAAAATTA
65 AGAGAAAATAATCTCAAGTAGATT--AAATTTGTT-TTAAGGAAAACTA
* *
353935 TCTCATGTGAGATC-AATTTTGTTTTTT
1 TCTCAAGTGAGA-CAAAATTTGTTTTTT
353962 TTGTGTGAAA
Statistics
Matches: 113, Mismatches: 18, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
108 4 0.04
110 71 0.63
111 38 0.34
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.38
Consensus pattern (110 bp):
TCTCAAGTGAGACAAAATTTGTTTTTTAGAGAAAACTATCTCAAGCAAGATAAAATTTGTTTTAA
GAGAAAATAATCTCAAGTAGATTAAATTTGTTTTAAGGAAAACTA
Found at i:355206 original size:23 final size:22
Alignment explanation
Indices: 355180--355223 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
355170 GTAGAATTAC
*
355180 ACCGAAGTGCCGTATAGAAATGG
1 ACCGAAGTGCCATATA-AAATGG
*
355203 ACCGGAGTGCCATATAAAATG
1 ACCGAAGTGCCATATAAAATG
355224 TTCATAAGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.36, C:0.18, G:0.27, T:0.18
Consensus pattern (22 bp):
ACCGAAGTGCCATATAAAATGG
Found at i:355253 original size:22 final size:21
Alignment explanation
Indices: 355228--355278 Score: 50
Period size: 22 Copynumber: 2.4 Consensus size: 21
355218 AAAATGTTCA
355228 TAAGGACCACATACAAATTCC
1 TAAGGACCACATACAAATTCC
* * * *
355249 TTAAGAATCATATACATATTCC
1 -TAAGGACCACATACAAATTCC
355271 -AAGGACCA
1 TAAGGACCA
355279 ATCATGTGTC
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
20 6 0.26
22 17 0.74
ACGTcount: A:0.43, C:0.24, G:0.10, T:0.24
Consensus pattern (21 bp):
TAAGGACCACATACAAATTCC
Found at i:356826 original size:44 final size:44
Alignment explanation
Indices: 356767--356854 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
356757 CATATACCTT
356767 AATTAGGTTGATGACAAGACAAATTTGGCTTCTAATTCTACTTA
1 AATTAGGTTGATGACAAGACAAATTTGGCTTCTAATTCTACTTA
356811 AATTAGGTTGATGACAAGACAAATTTGGCTTCTAATTCTACTTA
1 AATTAGGTTGATGACAAGACAAATTTGGCTTCTAATTCTACTTA
356855 TCAACTCTAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (44 bp):
AATTAGGTTGATGACAAGACAAATTTGGCTTCTAATTCTACTTA
Found at i:360366 original size:23 final size:23
Alignment explanation
Indices: 360322--360381 Score: 57
Period size: 23 Copynumber: 2.6 Consensus size: 23
360312 CAGCTTATAT
* * * *
360322 AAATACACTGAAGTGCCACGTAG
1 AAATGCACCGAAGTACCACGTAA
* *
360345 AATTGCACCGAAGTACCGCGTAA
1 AAATGCACCGAAGTACCACGTAA
*
360368 AAATGTACCGAAGT
1 AAATGCACCGAAGT
360382 GCCATATAAA
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.18
Consensus pattern (23 bp):
AAATGCACCGAAGTACCACGTAA
Found at i:360950 original size:17 final size:18
Alignment explanation
Indices: 360918--360956 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
360908 ATCTAATGTT
360918 ATTTATTTACTAAGTT-A
1 ATTTATTTACTAAGTTCA
* *
360935 ATTTATTTATTTAGTTCA
1 ATTTATTTACTAAGTTCA
360953 ATTT
1 ATTT
360957 CACATGACTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.59
Consensus pattern (18 bp):
ATTTATTTACTAAGTTCA
Found at i:366367 original size:22 final size:23
Alignment explanation
Indices: 366320--366375 Score: 78
Period size: 23 Copynumber: 2.5 Consensus size: 23
366310 GATTCCCTCC
*
366320 AGGGGGAATCGGTTCCCCTTCAA
1 AGGGGGAATCGGTTACCCTTCAA
*
366343 AGGGGGAATCGGTTACCCTT-TA
1 AGGGGGAATCGGTTACCCTTCAA
*
366365 AGGGGGTATCG
1 AGGGGGAATCG
366376 ATTCCTTCTG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 11 0.37
23 19 0.63
ACGTcount: A:0.21, C:0.20, G:0.36, T:0.23
Consensus pattern (23 bp):
AGGGGGAATCGGTTACCCTTCAA
Found at i:370180 original size:21 final size:20
Alignment explanation
Indices: 370140--370177 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
370130 AAGACTATTT
370140 TCATTTTTTATTTTGAAATA
1 TCATTTTTTATTTTGAAATA
370160 TCATTTTTTATTTTGAAA
1 TCATTTTTTATTTTGAAA
370178 ATAAAGTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.61
Consensus pattern (20 bp):
TCATTTTTTATTTTGAAATA
Found at i:372608 original size:152 final size:145
Alignment explanation
Indices: 372318--372615 Score: 524
Period size: 152 Copynumber: 2.0 Consensus size: 145
372308 TTTAGTAAGG
372318 ATTAAAATGAACTTTGAAAGACTTAGAGTAATATTTTGATATTCGAATAATTATCAAATACTTTA
1 ATTAAAATGAACTTTGAAAGACTTAGAGTAATATTTTGATATTCGAATAATTATCAAATACTTTA
372383 GAAACCTTTTGTAAATCTTAAATTCATTTAACTTAATTTGTTATATCGAAACATCAAAATGTTTT
66 GAAACCTTTTGTAAATCTTAAATTCATTTAACTTAATTTGTTATATCGAAACATCAAAATGTTTT
372448 CAACAAATGTGTTCC
131 CAACAAATGTGTTCC
372463 ATTAAAATGAACTTTGAAAGACTTAGAGTAATATTTTGATATTCGAATAATTATATCAAATATAC
1 ATTAAAATGAACTTTGAAAGACTTAGAGTAATATTTTGATATTCGAATAA-T-TATC-AA-ATAC
372528 TTTAGAAAACCTTTTGTAAAATCTTAAAATTCATTTAACTTAATTTGTTATATCGAAACATCAAA
62 TTTAG-AAACCTTTTGT-AAATCTT-AAATTCATTTAACTTAATTTGTTATATCGAAACATCAAA
*
372593 ATGTTTTCACCAAATGTGTTCC
124 ATGTTTTCAACAAATGTGTTCC
372615 A
1 A
372616 GTTTGGCTTC
Statistics
Matches: 145, Mismatches: 1, Indels: 7
0.95 0.01 0.05
Matches are distributed among these distances:
145 50 0.34
146 1 0.01
147 4 0.03
148 2 0.01
149 9 0.06
150 11 0.08
151 7 0.05
152 61 0.42
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.39
Consensus pattern (145 bp):
ATTAAAATGAACTTTGAAAGACTTAGAGTAATATTTTGATATTCGAATAATTATCAAATACTTTA
GAAACCTTTTGTAAATCTTAAATTCATTTAACTTAATTTGTTATATCGAAACATCAAAATGTTTT
CAACAAATGTGTTCC
Found at i:373283 original size:11 final size:10
Alignment explanation
Indices: 373266--373446 Score: 119
Period size: 10 Copynumber: 19.4 Consensus size: 10
373256 GTTTGATCGG
373266 TTTTCTTTCT
1 TTTTCTTTCT
373276 TCTTTCTTTCT
1 T-TTTCTTTCT
373287 TTACTT-TTTCT
1 TT--TTCTTTCT
373298 CTTTT-TTTCT
1 -TTTTCTTTCT
373308 TTTT-TTTC-
1 TTTTCTTTCT
373316 TTTT-TTTCT
1 TTTTCTTTCT
373325 TCTTT-TTT-T
1 T-TTTCTTTCT
*
373334 TTTTTTTTC-
1 TTTTCTTTCT
373343 TTTT-TTTCT
1 TTTTCTTTCT
* *
373352 TTTTTTTTTT
1 TTTTCTTTCT
373362 TTTTCTTT-T
1 TTTTCTTTCT
373371 TTTT-TTT-T
1 TTTTCTTTCT
* *
373379 TTTTTTTTTT
1 TTTTCTTTCT
* *
373389 TTTTTTTTTT
1 TTTTCTTTCT
373399 TTTTCTTT-T
1 TTTTCTTTCT
*
373408 TTGTC-TT-T
1 TTTTCTTTCT
373416 TTTTCTTT-T
1 TTTTCTTTCT
373425 TTTT-TTT-T
1 TTTTCTTTCT
373433 TTTTCTTTCT
1 TTTTCTTTCT
373443 TTTT
1 TTTT
373447 TGTGTGTTTT
Statistics
Matches: 151, Mismatches: 5, Indels: 30
0.81 0.03 0.16
Matches are distributed among these distances:
8 38 0.25
9 45 0.30
10 49 0.32
11 15 0.10
12 4 0.03
ACGTcount: A:0.01, C:0.11, G:0.01, T:0.88
Consensus pattern (10 bp):
TTTTCTTTCT
Found at i:373288 original size:8 final size:8
Alignment explanation
Indices: 373278--373447 Score: 190
Period size: 8 Copynumber: 21.2 Consensus size: 8
373268 TTCTTTCTTC
373278 TTTCTTTCT
1 TTTCTTT-T
*
373287 TTACTTTT
1 TTTCTTTT
*
373295 TCTCTTTT
1 TTTCTTTT
373303 TTTCTTTTT
1 TTTC-TTTT
373312 TTTCTTTTTT
1 TTTC--TTTT
373322 TCTTCTTTT
1 T-TTCTTTT
*
373331 TTTTTTTT
1 TTTCTTTT
373339 TTTCTTTT
1 TTTCTTTT
373347 TTTCTTTT
1 TTTCTTTT
*
373355 TTTTTTTT
1 TTTCTTTT
373363 TTTCTTTT
1 TTTCTTTT
373371 TTT-TTTT
1 TTTCTTTT
373378 TTT-TTTT
1 TTTCTTTT
373385 TTT-TTTT
1 TTTCTTTT
*
373392 TTTTTTTT
1 TTTCTTTT
373400 TTTCTTTT
1 TTTCTTTT
373408 TTGTCTTTT
1 TT-TCTTTT
373417 TTTC-TTT
1 TTTCTTTT
373424 TTT-TTTT
1 TTTCTTTT
*
373431 TTT-TTTC
1 TTTCTTTT
373438 TTTCTTTT
1 TTTCTTTT
373446 TT
1 TT
373448 GTGTGTTTTT
Statistics
Matches: 143, Mismatches: 11, Indels: 15
0.85 0.07 0.09
Matches are distributed among these distances:
7 39 0.27
8 68 0.48
9 27 0.19
10 6 0.04
11 3 0.02
ACGTcount: A:0.01, C:0.10, G:0.01, T:0.89
Consensus pattern (8 bp):
TTTCTTTT
Found at i:373311 original size:17 final size:17
Alignment explanation
Indices: 373266--373446 Score: 207
Period size: 17 Copynumber: 10.8 Consensus size: 17
373256 GTTTGATCGG
373266 TTTTCTTTCTTCTTTCTTT
1 TTTTCTTT-TT-TTTCTTT
* *
373285 CTTTAC-TTTTTCTCTTT
1 -TTTTCTTTTTTTTCTTT
373302 TTTTCTTTTTTTTCTTT
1 TTTTCTTTTTTTTCTTT
373319 TTTTCTTCTTTTTT-TTT
1 TTTTCTT-TTTTTTCTTT
*
373336 TTTTTTCTTTTTTTCTTT
1 TTTTCT-TTTTTTTCTTT
373354 TTTT-TTTTTTTTC-TT
1 TTTTCTTTTTTTTCTTT
373369 TTTT-TTTTTTTT-TTT
1 TTTTCTTTTTTTTCTTT
373384 TTTT-TTTTTTTT-TTT
1 TTTTCTTTTTTTTCTTT
*
373399 TTTTCTTTTTTGTCTTT
1 TTTTCTTTTTTTTCTTT
*
373416 TTTTCTTTTTTTTTTTT
1 TTTTCTTTTTTTTCTTT
373433 TTTTCTTTCTTTTT
1 TTTTCTTT-TTTTT
373447 TGTGTGTTTT
Statistics
Matches: 145, Mismatches: 8, Indels: 18
0.85 0.05 0.11
Matches are distributed among these distances:
15 35 0.24
16 19 0.13
17 64 0.44
18 21 0.14
19 2 0.01
20 4 0.03
ACGTcount: A:0.01, C:0.11, G:0.01, T:0.88
Consensus pattern (17 bp):
TTTTCTTTTTTTTCTTT
Found at i:373354 original size:44 final size:42
Alignment explanation
Indices: 373299--373446 Score: 208
Period size: 44 Copynumber: 3.4 Consensus size: 42
373289 ACTTTTTCTC
373299 TTTTTTTCTTTTTTTTCTTTTTTTCTTCTTTTTTTTTTTTTTT
1 TTTTTTTCTTTTTTTTCTTTTTTTCTT-TTTTTTTTTTTTTTT
373342 CTTTTTTTCTTTTTTTT-TTTTTTTCTTTTTTTTTTTTTTTTTTTT
1 -TTTTTTTCTTTTTTTTCTTTTTTTC---TTTTTTTTTTTTTTTTT
* *
373387 TTTTTTTTTTTTTTTTCTTTTTTGTCTTTTTTTCTTTTTTTTT
1 TTTTTTTCTTTTTTTTCTTTTTT-TCTTTTTTTTTTTTTTTTT
373430 TTTTTTTCTTTCTTTTT
1 TTTTTTTCTTT-TTTTT
373447 TGTGTGTTTT
Statistics
Matches: 95, Mismatches: 3, Indels: 12
0.86 0.03 0.11
Matches are distributed among these distances:
43 34 0.36
44 36 0.38
45 21 0.22
46 4 0.04
ACGTcount: A:0.00, C:0.08, G:0.01, T:0.91
Consensus pattern (42 bp):
TTTTTTTCTTTTTTTTCTTTTTTTCTTTTTTTTTTTTTTTTT
Found at i:373447 original size:17 final size:16
Alignment explanation
Indices: 373266--373447 Score: 192
Period size: 15 Copynumber: 11.2 Consensus size: 16
373256 GTTTGATCGG
* * *
373266 TTTTCTTTCTTCTTTC
1 TTTTTTTTCTTTTTTT
* *
373282 TTTCTTTACTTTTTCTCT
1 TTTTTTTTCTTTTT-T-T
373300 TTTTTTCTT-TTTTTTCT
1 TTTTTT-TTCTTTTTT-T
373317 TTTTTTCTTCTTTTTTT
1 TTTTTT-TTCTTTTTTT
373334 TTTTTTTTCTTTTTTT
1 TTTTTTTTCTTTTTTT
*
373350 CTTTTTTT-TTTTTTT
1 TTTTTTTTCTTTTTTT
*
373365 TCTTTTTT-TTTTTTT
1 TTTTTTTTCTTTTTTT
373380 TTTTTTTT-TTTTTTT
1 TTTTTTTTCTTTTTTT
373395 TTTTTTTTCTTTTTTGT
1 TTTTTTTTCTTTTTT-T
*
373412 CTTTTTTTCTTTTTTTT
1 TTTTTTTTC-TTTTTTT
*
373429 TTTTTTTTCTTTCTTT
1 TTTTTTTTCTTTTTTT
373445 TTT
1 TTT
373448 GTGTGTTTTT
Statistics
Matches: 145, Mismatches: 14, Indels: 14
0.84 0.08 0.08
Matches are distributed among these distances:
15 42 0.29
16 42 0.29
17 38 0.26
18 22 0.15
19 1 0.01
ACGTcount: A:0.01, C:0.11, G:0.01, T:0.88
Consensus pattern (16 bp):
TTTTTTTTCTTTTTTT
Found at i:373457 original size:70 final size:68
Alignment explanation
Indices: 373291--373458 Score: 148
Period size: 62 Copynumber: 2.6 Consensus size: 68
373281 CTTTCTTTAC
* * * * *
373291 TTTTTC-TCTTTTTTTCTTTT-TTTTCTTTTTT-TCT-TCTTTTTT-TT-TTTTTTTCTTTTTTT
1 TTTTTCTTTTTTTTTTTTTTTCTTTTCTTTTTTGTGTGTTTTTTTTCTTCTTTTTTTTTTTTTTT
373350 CTT
66 CTT
* * *
373353 TTTTT-TTTTTTTTCTTTTTTT-TTTT-TTTTTT-T-TTTTTTTTTT-TT-TTTTTTCTTTTTTG
1 TTTTTCTTTTTTTT-TTTTTTTCTTTTCTTTTTTGTGTGTTTTTTTTCTTCTTTTTTTTTTTTTT
373411 TCTT
65 TCTT
373415 TTTTTCTTTTTTTTTTTTTTT-TCTTTCTTTTTTGTGTGTTTTTT
1 TTTTTCTTTTTTTTTTTTTTTCT-TTTCTTTTTTGTGTGTTTTTT
373459 CCGTGTTGTC
Statistics
Matches: 91, Mismatches: 7, Indels: 12
0.83 0.06 0.11
Matches are distributed among these distances:
61 1 0.01
62 55 0.60
63 21 0.23
64 6 0.07
65 1 0.01
66 7 0.08
ACGTcount: A:0.00, C:0.08, G:0.02, T:0.89
Consensus pattern (68 bp):
TTTTTCTTTTTTTTTTTTTTTCTTTTCTTTTTTGTGTGTTTTTTTTCTTCTTTTTTTTTTTTTTT
CTT
Found at i:373458 original size:1 final size:1
Alignment explanation
Indices: 373299--373447 Score: 181
Period size: 1 Copynumber: 149.0 Consensus size: 1
373289 ACTTTTTCTC
* * * * * *
373299 TTTTTTTCTTTTTTTTCTTTTTTTCTTCTTTTTTTTTTTTTTTCTTTTTTTCTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * *
373364 TTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTTTTTGTCTTTTTTTCTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* *
373429 TTTTTTTTCTTTCTTTTTT
1 TTTTTTTTTTTTTTTTTTT
373448 GTGTGTTTTT
Statistics
Matches: 122, Mismatches: 26, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
1 122 1.00
ACGTcount: A:0.00, C:0.08, G:0.01, T:0.91
Consensus pattern (1 bp):
T
Found at i:373458 original size:27 final size:23
Alignment explanation
Indices: 373291--373447 Score: 201
Period size: 23 Copynumber: 6.7 Consensus size: 23
373281 CTTTCTTTAC
*
373291 TTTTTCTCTTTTTTTCTTTTTTTT
1 TTTTTCT-TTTTTTTTTTTTTTTT
* * *
373315 CTTTT-TTTCTTCTTTTTTTTTT
1 TTTTTCTTTTTTTTTTTTTTTTT
373337 TTTTTCTTTTTTTCTTTTTTTTTT
1 TTTTTCTTTTTTT-TTTTTTTTTT
373361 TTTTTCTTTTTTTTTTTTTTTTT
1 TTTTTCTTTTTTTTTTTTTTTTT
373384 TTTTT-TTTTTTTTTTTTTTCTTT
1 TTTTTCTTTTTTTTTTTTTT-TTT
*
373407 TTTGTCTTTTTTTCTTTTTTTTTTT
1 TTTTTC-TTTTTT-TTTTTTTTTTT
*
373432 TTTTTCTTTCTTTTTT
1 TTTTTCTTTTTTTTTT
373448 GTGTGTTTTT
Statistics
Matches: 117, Mismatches: 10, Indels: 13
0.84 0.07 0.09
Matches are distributed among these distances:
22 31 0.26
23 32 0.27
24 32 0.27
25 14 0.12
26 8 0.07
ACGTcount: A:0.00, C:0.09, G:0.01, T:0.90
Consensus pattern (23 bp):
TTTTTCTTTTTTTTTTTTTTTTT
Found at i:376784 original size:9 final size:9
Alignment explanation
Indices: 376767--376800 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
376757 TAAAAAAAGA
*
376767 AATTCATCC
1 AATTTATCC
376776 AATTTATCC
1 AATTTATCC
376785 AATTTATCC
1 AATTTATCC
*
376794 AAATTAT
1 AATTTAT
376801 ATATGATTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.38, C:0.21, G:0.00, T:0.41
Consensus pattern (9 bp):
AATTTATCC
Found at i:377389 original size:19 final size:18
Alignment explanation
Indices: 377362--377398 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
377352 CAATACATGT
*
377362 AGTATTATATATATAATAA
1 AGTAATATATA-ATAATAA
377381 AGTAATATATAATAATAA
1 AGTAATATATAATAATAA
377399 TGTACGTGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (18 bp):
AGTAATATATAATAATAA
Found at i:382965 original size:18 final size:17
Alignment explanation
Indices: 382934--382967 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
382924 TTTTATGTGA
382934 TTTTCTTCTCTGATTGC
1 TTTTCTTCTCTGATTGC
*
382951 TTTTCTTTCTTTGATTG
1 TTTTC-TTCTCTGATTG
382968 ATTTGTGACA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.06, C:0.18, G:0.12, T:0.65
Consensus pattern (17 bp):
TTTTCTTCTCTGATTGC
Found at i:385115 original size:21 final size:21
Alignment explanation
Indices: 385083--385141 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
385073 ATTTACCGTG
* *
385083 ATTGCGGCCGTCGCGGGCGTT
1 ATTGAGGCCGTCGCGGGCGCT
* *
385104 ATTGAGGTCGTCGCGGACGCT
1 ATTGAGGCCGTCGCGGGCGCT
*
385125 ATTGCGGCCGTCGCGGG
1 ATTGAGGCCGTCGCGGG
385142 TAACTCGGAC
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.08, C:0.27, G:0.42, T:0.22
Consensus pattern (21 bp):
ATTGAGGCCGTCGCGGGCGCT
Found at i:385559 original size:94 final size:94
Alignment explanation
Indices: 385398--385585 Score: 376
Period size: 94 Copynumber: 2.0 Consensus size: 94
385388 CAGCAAACTT
385398 GGCTCTTAAATCACTGAAATCAACCCCATTTGCTGCAAGAAAAAGCATCCCTGTACTGATCAATG
1 GGCTCTTAAATCACTGAAATCAACCCCATTTGCTGCAAGAAAAAGCATCCCTGTACTGATCAATG
385463 ACCACGGACGGATACTAAGTATCCCTGTA
66 ACCACGGACGGATACTAAGTATCCCTGTA
385492 GGCTCTTAAATCACTGAAATCAACCCCATTTGCTGCAAGAAAAAGCATCCCTGTACTGATCAATG
1 GGCTCTTAAATCACTGAAATCAACCCCATTTGCTGCAAGAAAAAGCATCCCTGTACTGATCAATG
385557 ACCACGGACGGATACTAAGTATCCCTGTA
66 ACCACGGACGGATACTAAGTATCCCTGTA
385586 TGTTGAACTC
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
94 94 1.00
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (94 bp):
GGCTCTTAAATCACTGAAATCAACCCCATTTGCTGCAAGAAAAAGCATCCCTGTACTGATCAATG
ACCACGGACGGATACTAAGTATCCCTGTA
Found at i:388792 original size:631 final size:623
Alignment explanation
Indices: 387598--388851 Score: 2377
Period size: 631 Copynumber: 2.0 Consensus size: 623
387588 AAATTAAATT
387598 TGAGTGTGGTTGAAAATAATTATCTTTTATTATAAACGAATTATGAATCTTTTCCTTTCAACCAA
1 TGAGTGTGGTTGAAAATAATTATCTTTTATTATAAACGAATTATGAATCTTTTCCTTTCAACCAA
387663 AATAAACGAAAAAAGAAATTACTCTTAGATTTCAGTCCTCAACAAAAAATTTTCTCACTTCTTGA
66 AATAAACGAAAAAAGAAATTACTCTTAGATTTCAGTCCTCAACAAAAAATTTTCTCACTTCTTGA
387728 GTAGAGATGGTGATATCTCTACACTCTTGCCTTCATTGCTTTCTTCTCAAAATACTAATCCCAAC
131 GTAGAGATGGTGATATCTCTACACTCTTGCCTTCATTGCTTTCTTCTCAAAATACTAATCCCAAC
387793 TCAACCCAATTTCCAAACCATCAAAAGCTATAATTCACCCCCATTCCAACTTCAAATCCCTCAAA
196 TCAACCCAATTTCCAAACCATCAAAAGCTATAATTCACCCCCATTCCAACTTCAAATCCCTCAAA
387858 ATCCTAATTGCACAGTCCTCAATCTTCACCAAACTTCAAAAGCCCACCTTTCAATCCATCCACAT
261 ATCCTAATTGCACAGTCCTCAATCTTCACCAAACTTCAAAAGCCCACCTTTCAATCCATCCACAT
387923 TCCACATTTCCCGCTAAAATTCCAAACCTTTTGGTGTTCAAGATAGAAAATGCGACAACTTTAGG
326 TCCACATTTCCCGCTAAAATTCCAAACCTTTTGGTGTTCAAGATAGAAAATGCGACAACTTTAGG
387988 TCCAAGGAATCAATTTCAAGTACTTAAGCGATATGGGGTTAAAGAATCCGAGGACACCGAAAAAG
391 TCCAAGGAATCAATTTCAAGTACTTAAGCGATATGGGGTTAAAGAATCCGAGGACACCGAAAAAG
388053 TGGTGGACTCTGATGGAGGCGGAGGCGGCGGCGGAGATGGAGACGATGGAGAGGTAGAGATGAAA
456 TGGTGGACTCTGATGGAGGCGGAGGCGGCGGCGGAGATGGAGACGATGGAGAGGTAGAGATGAAA
388118 AGTGGGTCAGTGCCAGAATGGTTGAATGTCACTCCTGATGATGCAAAAACGGTTATTGCTGCTGT
521 AGTGGGTCAGTGCCAGAATGGTTGAATGTCACTCCTGATGATGCAAAAACGGTTATTGCTGCTGT
388183 GGTAATATCGCTTGCTTT-CGAGCATTCGTGGCTGAGC
586 GGTAATATCGCTTGCTTTCCGAGCATTCGTGGCTGAGC
*
388220 TGAGTGTGGTTGAAAATAATTATCTTTTATTATAAACGAATTATGAATCTTTTCTTTTCAACCAA
1 TGAGTGTGGTTGAAAATAATTATCTTTTATTATAAACGAATTATGAATCTTTTCCTTTCAACCAA
388285 AATAAACGAAAAAAGAAATTATACTCTTAGATTTCAGTCCTCAAC-AAAAATTTTCTCACCTTCT
66 AATAAACGAAAAAAGAAA-T-TACTCTTAGATTTCAGTCCTCAACAAAAAATTTTCTCA-CTTC-
388349 TTGAGTAGAGATGGTGATATCTCTACACTCTTTGCCTTCATTGCTTTCTTCTCAAAATACTAATC
127 TTGAGTAGAGATGGTGATATCTCTACACTC-TTGCCTTCATTGCTTTCTTCTCAAAATACTAATC
388414 CCAACTCAACCCAATTTTCCAAACCCATCAAAAGCTATAATTTCACCCCCATTCCCAACTTCAAA
191 CCAACTCAACCCAA-TTTCCAAA-CCATCAAAAGCTATAA-TTCACCCCCATT-CCAACTTCAAA
*
388479 TCCCTCAAAATCCCTAATTGCACAGTCCTCAATCTTCACCAAACTTCAAAATCCCACCTTTCAAT
252 TCCCTCAAAAT-CCTAATTGCACAGTCCTCAATCTTCACCAAACTTCAAAAGCCCACCTTTCAAT
*
388544 CCATCCCCATTCCACATTTCCCGCTAAAATTCCAAACCTTTTGGTGTTCAAGATAGAAAATGCGA
316 CCATCCACATTCCACATTTCCCGCTAAAATTCCAAACCTTTTGGTGTTCAAGATAGAAAATGCGA
388609 CAACTTTAGGTCCAAGGAATCAATTTCAAGTACTTAAGCGATATGGGGTTAAAGAATCCGAGGAC
381 CAACTTTAGGTCCAAGGAATCAATTTCAAGTACTTAAGCGATATGGGGTTAAAGAATCCGAGGAC
388674 ACCGAAAAAGTGGTGGACTCTGATGGAGGCGGAGGCGGCGGCGGAGATGGAGACGATGGAGAGGT
446 ACCGAAAAAGTGGTGGACTCTGATGGAGGCGGAGGCGGCGGCGGAGATGGAGACGATGGAGAGGT
388739 AGAGATGAAAAGTGGGTCAGTGCCAGAATGGTTGAATGTCACTCCTGATGATGCAAAAACGGTTA
511 AGAGATGAAAAGTGGGTCAGTGCCAGAATGGTTGAATGTCACTCCTGATGATGCAAAAACGGTTA
388804 TTGCTGCTGTGGTAATATCGCTTGCTTTCCGAGCATTCGTGGCTGAGC
576 TTGCTGCTGTGGTAATATCGCTTGCTTTCCGAGCATTCGTGGCTGAGC
388852 CGAGGTACAT
Statistics
Matches: 618, Mismatches: 3, Indels: 12
0.98 0.00 0.02
Matches are distributed among these distances:
622 82 0.13
623 14 0.02
624 28 0.05
625 30 0.05
626 48 0.08
627 8 0.01
628 16 0.03
629 12 0.02
630 22 0.04
631 339 0.55
632 19 0.03
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (623 bp):
TGAGTGTGGTTGAAAATAATTATCTTTTATTATAAACGAATTATGAATCTTTTCCTTTCAACCAA
AATAAACGAAAAAAGAAATTACTCTTAGATTTCAGTCCTCAACAAAAAATTTTCTCACTTCTTGA
GTAGAGATGGTGATATCTCTACACTCTTGCCTTCATTGCTTTCTTCTCAAAATACTAATCCCAAC
TCAACCCAATTTCCAAACCATCAAAAGCTATAATTCACCCCCATTCCAACTTCAAATCCCTCAAA
ATCCTAATTGCACAGTCCTCAATCTTCACCAAACTTCAAAAGCCCACCTTTCAATCCATCCACAT
TCCACATTTCCCGCTAAAATTCCAAACCTTTTGGTGTTCAAGATAGAAAATGCGACAACTTTAGG
TCCAAGGAATCAATTTCAAGTACTTAAGCGATATGGGGTTAAAGAATCCGAGGACACCGAAAAAG
TGGTGGACTCTGATGGAGGCGGAGGCGGCGGCGGAGATGGAGACGATGGAGAGGTAGAGATGAAA
AGTGGGTCAGTGCCAGAATGGTTGAATGTCACTCCTGATGATGCAAAAACGGTTATTGCTGCTGT
GGTAATATCGCTTGCTTTCCGAGCATTCGTGGCTGAGC
Found at i:390712 original size:56 final size:56
Alignment explanation
Indices: 390626--390739 Score: 228
Period size: 56 Copynumber: 2.0 Consensus size: 56
390616 CTTGAGCGTG
390626 GCTGTGCTATTGACAAGCAGCAGGAGAGTGTCAAAGCATCTGAATAGATGTATTCA
1 GCTGTGCTATTGACAAGCAGCAGGAGAGTGTCAAAGCATCTGAATAGATGTATTCA
390682 GCTGTGCTATTGACAAGCAGCAGGAGAGTGTCAAAGCATCTGAATAGATGTATTCA
1 GCTGTGCTATTGACAAGCAGCAGGAGAGTGTCAAAGCATCTGAATAGATGTATTCA
390738 GC
1 GC
390740 CTTACTGATT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 58 1.00
ACGTcount: A:0.32, C:0.17, G:0.27, T:0.25
Consensus pattern (56 bp):
GCTGTGCTATTGACAAGCAGCAGGAGAGTGTCAAAGCATCTGAATAGATGTATTCA
Done.